My party also prefers to see dice rolled in the open, so I've had to learn to creatively doctor encounters myself.
Change the Numbers
Instead of changing your rolls, change the numbers you're adding to the rolls or comparing the rolls to. If you feel you have to justify this, perhaps monster's so mad it takes a penalty to attacks and defenses, or the party has been given a temporary boon from the ghost of the monster's previous victim. Feel free to adjust hit points too: the only time the party has a sense of how many hit points the monster has left is when you declare it bloodied. If you change the hit point total before that point it's impossible to detect; if you change it after... the party probably won't notice and really shouldn't complain if they do.
Word of experience: If your party likes to use knowledge of dice rolls to extrapolate monster defenses and attack modifiers, they'll call you on this. Have a justification ready, or say "oops, let me check my math" and then move on to one of the other points on this list.
Fight Dumb
- Be less careful about getting flanked. Give the party a free +2 to hit!
- Provoke more opportunity attacks. Easy way to get the fight over faster. Don't forget that some circumstantial damage bonuses (like sneak attack) are per-turn instead of per-round, so combine this with the above point.
- Make poor tactical decisions, like triggering mark punishment when you don't have to. Defenders love it when you do that.
The other side of Fight Dumb is:
Meta Smart (reward your party for their choices)
- Use your debuff attacks against PCs who won't take it as hard (e.g., daze the guy with Superior Will).
- Take advantage of PCs traits to deal less damage. Set the tiefling on fire; he'll enjoy not caring. If a PC has poison resist, have the NPC take a small action to poison his blade (add the poison keyword to his attacks); suddenly the PC is taking less damage and feels good about his resist choice.
- Target high defenses. Go for the cleric's Will, the fighter's Fortitude, the paladin's AC. Missing deals a lot less damage, and makes the party feel cool.
- Don't forget that trained knowledge checks can grant a PC limited knowledge of a creature's stats. Encourage this and reward it; perhaps the monster has a vulnerability they haven't been taking advantage of (perhaps you just made it up now!). I've been known to also grant small bonuses to attack or damage with knowledge checks, but don't make that a regular thing. Be creative with this one: maybe this particular monster can't make the enormous swings it's used to if its target is near blocking terrain, so it takes a penalty to attack PCs adjacent to walls. Or maybe the monster has poor peripheral vision and grants a +3 to flankers instead of +2, if you decide the party needs a bump in their to-hit?
Use Terrain
Before your next session, take look at the many terrain options 4e offers. Many of them can grant advantages and turn the tide of battles if used creatively, and they can inspire you to make your own terrain features as well. The crumbled remains of a holy shrine that gives a healing bonus to those nearby might be just what your fight needs; call for a Religion/History/Perception check to suddenly discover it in the middle of battle (maybe it lights up when a bloodied creature gets near?).
Don't Be Afraid to Call a Fight
Your monsters probably don't want to die. Some or all of them might surrender or run away when bloodied or when their friends drop. This shortens fights considerably, provides RP in battles and makes the world and its inhabitants more real.
Design Philosophies Have Changed
Around the time the Monster Manual 3 was published, 4e monster design underwent a drastic shift. Among other things, damage increased and hp dropped: this encourages faster, more intense fights. I don't feel competent to discuss the maths, so here are relevant posts:
Come Clean
It goes against generations worth of the DM vs Players mindset, but you could just be straightforward with your party: You're a new GM and learning the ropes, and sometimes you're going to try things that don't work. You can ask them to be understanding as you adjust things when you realize they don't work as intended, and you might even benefit from their direct input.
It sounds like they're having trouble because they can't figure out where the plot is. Their actions make it clear they would like to fight chaos, but in the absence of chaos to fight, they're filling time by lining their own pockets.
You've already made some progress toward the solution by giving them criminal organizations to destroy. It sounds like they really got into that and had fun with it. You should do more of that, but bigger. (What's the intended plot for your campaign? Why haven't they run into that yet?) If you keep giving them interesting things to do, they'll lose interest in robbing the city.
Best Answer
I have never GMed pathfinder, but I understand it is extremely similar to DnD where I have a fair bit of experience.
Make it fit the encounter
I generally try to make the treasure fit the encounter in the sense that the treasure should be what the creature would logically have. Under most circumstances that means I totally ignore both what the players want and the wealth by level as well as the guidelines.
So, the phase spiders you mentioned would likely have nothing but their venom. A group of goblins would have some simple spears and some simple bows and arrows. For things like that, loot is fairly simple to come up with on the fly as "What would they have?"
A group of full on humanoids is more intersting as those tend to come with equipment, but then the group finds the equipment they were using pluse whatever loot the bandits collected so far. That of course is a bit harder to come up with on the fly, but I'm still being guided by quickly thinking of what equipment did I have them use and what would they likely have.
Now of course, someone might come back by pointing out (as some players have with me) that those threats can kill adventurers and might have some adventurer equipment, so occassionally I sprinkle in something else, but then I literally just make it up on the spot and it is normally generic and low level (after all, if the adventurer that encountered these things before was powerful enough to defeat it or even get away, that equipment wouldn't be there now, so the equipment they find from random encounters will always be much weaker than what they have.)
Quests
I think that scheme has the advantage of keeping things realistic and for most encounters, especially the occassional random encounter, and makes loot easy to generate on the fly. But it has the horrible disadvantage of making meaningful loot from that kind of encounter nearly nonexistent and would leave them way behind in the wealth by level charts.
But when I GM I generally expect the players to get most of their wealth through quests. Most quests will come in the form of someone hiring the band of heroes and paying them very well for their services. If the employer/quest-giver is well connected the heroes might be able to directly bargain with the employer to get them a hard to acquire item they want in place of some of the gold initially offered.
When the story says that the quest-giver can't pay them well because they are poor themselves, then I have the quest giver reward them with information which leads to another quest which has a direct payoff. For instance, an old widow's son has been turned into a lycanthrope. The heroes rescue him and turn him back. The old widow can't pay them directly, but she knows the old local story about the Archmage Generet from over 200 years ago who died leaving behind his tower. The tower is reputed to hold his great wealth but remains home to the remains of his experiments so it is too dangerous for any of the locals to go to.
The loot from the tower will fit with what an archamge would likely have lying around and is meant to compensate for the work on the lycanthrope so it will be far richer than the threat level of the gaurdians would suggest by the book. But I still fill it by thinking mostly about the kinds of things an archmage would have lying around. They will find things like potions, wands, components, and scrolls in abundance, but probably not a set of plate mail. If they want a set of enchanged plate mail, they will either sell off the loot to buy it or else they will start asking around specifically for a lead to that sort of quest.
Getting them what they want
Which brings me to leads. In games I run, the players buy most of the equipment they specifically want. But if they want something truly exotic where buying it won't work and they can't negotiate for it from a quest giver, then they need to look for a lead. A lead is normally the start of quest meant to bring them to exactly what they want.
So, the Paladin needs a new set of armor, but not just any set, he wants a legendary one. His player tells me ooc, and in character starts asking around. No one can sell him something like that, but eventually someone will tell him the story of Sir Gawain the Kind who was killed by the dragon Karlesto. Sir Gawain had a set and it likely is now in Karlesto's possession. No one is paying to have the dragon killed because it has been inactive for decades...but if they do kill it they will likely find his set of armor along with the gold the dragon has been hoarding.