I've had player conflict from time to time. Sometimes it can be handled simply, by talking to them. Be direct - as the GM, you're the leader, and it's your game. "Your fighting makes everyone else not have a good time. I'm the GM, and I'm telling you now to shape up and not bring your beefs into the game."
Look for opportunities to have them play in different games. Most groups I'm in end up having several concurrent games going on on different days or whatever, so people can stay "in the group" but not play with people that bug them. Once, to accommodate differing play styles among the group, I split the campaign and ran two different games on two different days for the two different groups.
Also, sometimes you can address it in game. I had a player who I nearly kicked out, because he would throw fits that were arguably in character but really boiled over to out of character very quickly. (This one time, he was so agitated at the group not taking the thousands of copper pieces from a dead orc tribe that after a screaming fit he just ran into a wraith and suicided.) I ended up giving him a reason to subtly spy on the other players and that sublimated his desire for conflict in a way that didn't have negative group consequences. Perhaps there's ways to sublimate their conflict in the same way. If you disallow table talk, for example, they will have to communicate in character, and arguments in character tend to get you ambushed by bad guys, tossed in dungeons, etc.
In the end, you may have to eject one or both players from your group. Geeks tend to Marty McFly about this too much and not address problems directly, read the Five Geek Social Fallacies for some insight into this (though bands, sports teams, etc. end up having the same problems frequently).
In my current group, we had a player who was just such a total goon that no one enjoyed games that he attended. People tried working with him, but finally we all got together and discussed the problem and ended up voting to disinvite him from the game. "He's making the game less fun" is more than enough justification.
In this case it's harder - is one person really the problem? Or is it both of them, but they're fine if the other isn't there? If they are both a joy to game with except when the other player's there, it's hard to decide which one to punt, but you can just leave it up to them. "Look, we like gaming with both of you, but it's unacceptable and fun-killing when y'all fight. Whoever starts it next time will need to leave." You can try giving people "time outs" short of punting them from the group - "You have to leave this session now because you're fighting." See if that shapes them up. I don't know how much you have invested in these people and how much work is justified to save the group vs. ditching one or more of the members out of hand. It's easy to be an Internet Tough Guy and say "throw them out, then ostracize them from your life!" because it's easy to say that when it's not you in that place. Don't jump to ejection before bothering to talk with friends, but also don't be afraid to pull the trigger once it's clear that's the only thing that will make the game fun again.
How To Learn To GM
There are a variety of resources nowadays that can help you accomplish this. There are also many existing questions on this site about GMing that will point you to more content than you can ever consume.
Watch
In your question, you mention wanting to see more examples of real play. There's a number of ways to do so.
Actual Play Resources
- Podcasts capture the entire play session. There's video podcasts too like on Twitch. See Where can I find actual play podcasts for RPGs?
- Session Summaries (aka Actual Plays, Story Hours, Campaign Journals) usually are severely abridged, but leave out a lot of the cruft. See Where can I find transcripts of actual game sessions? and Where to find game session reports?
- Blogs. There's a million blogs about how to GM. Start with the RPG Bloggers Network. Go to the blogrolls of blogs you like to find more like them. Focus in on blogs about your chosen game(s) and play style(s).
- Play by post forums. If you want to watch people actually play in text, there's a million of these too. Many dedicated sites, specific forums on RPG.net, ENWorld, Paizo, etc. In fact, RP-by-post is very popular even when not affiliated with a proper RPG/ruleset.
- Sit in. There are plenty of other people running games, some in public places like your friendly local game store (D&D Encounters, Pathfinder Society) and conventions. See below under "Play" though, if you're going to the effort of being there you need to stop being a wallflower and get on in and play.
Some games also have better advice sections than others - see What role-playing games have good gamemaster advice sections?
Play
In the end though just watching is not the most effective approach to learning. Watching games is less useful experience than actually being in one. Have you considered playing in those games before running them to learn from other GMs? It's reasonably easy to find other gaming groups, you don't have to abandon yours to play in another. Where can I find other RPG players?
Go to RPG conventions, find games at gaming stores, play on forums or G+ (see also Finding online RPG players for a play-by-chat RPG Campaign?) - just get more experience. The GM was often called the "judge" in the old days, and in the legal world you need to spend a lot of time being a lawyer before you make a good judge. You need to spend some time playing to become a good GM. If you can't think how the players will proceed in a given situation, you need more play time.
Read
There are many books on GMing - see What is the single most influential book every GM should read?
Also try watching/reading relevant genre media. "I don't get how to put together a story" should get its first-order correction by consuming some of that genre and looking at the stories.
Learn
A lot of the problem you seem to be experiencing is pure storytelling. Try How do I get better at narrating/storytelling as a GM? and As a GM, how can I create and role-play diverse NPCs better? Read up on the specific aspects of GMing you feel you're not good at, there's plenty here. Try questions tagged with the gm-techniques tag. Feel free and ask questions here as well about specific aspects of GMing.
There are also a large, large number of RPG forums out there in the world, for every game and type of gaming. If you don't understand something someone posts, you can easily reply and ask.
Do
aka How I Learned To GM
We didn't have these newfangled Interwebs when I was a kid. I GMed almost before I ever played. I did play in a very informal game of D&D in a car on the way to Scout camp, no dice, PvP, everyone had artifact weapons. But other than that, I started out as a GM. I bought a sci-fi RPG (Star Frontiers) without knowing anything about it (I had bought and played a little TSR chit game, Star Force, and was looking for other fun stuff from the same company). None of my friends were interested in GMing and I was in a small Texas town that didn't have conventions or whatnot - life was less mobile and connected back then. So I just read the game books and then ran games for my friends. And I kept running them, and learned from my mistakes and corrected. I read comics and science fiction avidly, so characters and plots weren't that hard to devise. Beyond that, I just learned the way you learn to do anything through practice, whether it's a sport, writing, a musical instrument... How-to's and YouTube videos are cute jumpstarters nowadays, but "Do, and learn from doing" has yet to be eclipsed in being the primary way to actually become good at something.
Fear of "making a mistake" is the dumbest and most paralyzing instinct you can have in life. In a video game you're going to die a couple times off the bat; in baseball you're going to swing and miss a lot before you hit; in baking you're gonna burn some cookies. But you learn through those mistakes. It's fine to do a little reading up ahead of time but the only way to become good, really, is get your butt in gear and do it.
Best Answer
The scale and power of the Big Ten should not be undersold. Nor should the power and insanity that one experiences with a Horror. Shadowrunners are just a bunch of dudes, really. They're just really good and professional dudes. Ticking off the different corps or governments of the world can and will buy retribution from those corps if the cred is enough. And having the prison being a major hub of the players and where they are kept, there's a really good answer to this.
Have a mega corp purchase the Shadowrunners.
Honestly, this is the natural progression of your game. You are having the runners hit a Karma level that screams retirement or world-changing efforts. They can't continue to play as random chaos anymore. They are too powerful to continue to ignore, from a mega corp standpoint, and are good only two ways. Theirs or dead. The runners have shown Saeder-Krupp that they are good and can piss off a great dragon. If I was running Lofwyr as a business man, I would see the potential that these runners could offer, given that I could buy and contain them. Else, I'd just buy them to have them executed to get them out of my hair. As a great dragon that's in charge of the most profitable Big Ten in the world, I have so much cred that I can throw at a problem, I might as well bury the players in mountains of it to suffocate them.
Really, the best you can do at this point is show the runners that they can't be ignored anymore. No matter the power level of a PC in Shadowrun, there is always something bigger, tougher, and meaner. I'd go so far as to tell you to sic a cyber zombie or two on them. Not the player driven ones, but an honest to god walking abomination of magic and technology. From the flavor of the game and the durability and deadliness of it, it's the perfect thing to send at the players if you want to test them at this point. And most corps can claim to have one in their back reserves to clean up messes like your Shadowrun team if they absolutely have to.
But even if they can down the cyber-zombie, there's still the question of where they go. And honestly, I think it's time to roll new characters. A year-long campaign that's sprouted a few 250 karma players means it's time for a change of scenery. Have the runners take on their last challenge, break free from the prison they've been in or die trying, and retire the campaign. Keep all the flavor, even put some of the old PC's in as NPCs in the world if they survive, and roll up new characters. It's the kind of thing I see and say "It's been a good run, so let's go out in the biggest bang we can and start fresh". But, again, that's my two cents on if I was running the game.