How to manage loot when doing missions in fleet

Low-level missions are not very lucrative, but you still shouldn't make a loss on them if you are doing them properly. Level 3 missions should earn you okay money, but to make a reasonable amount of money for your time you need to fly level 4 missions.

If you fly a shield-tanked ship (I assume you're still flying a Caracal), you shouldn't let yourself get shot into armor. Just warp out and dock at a station to fill up your shields quickly again. Your only cost should be your ammunition. Some missions are harder, and you'll have some difficulties in the beginning when you're still learning, but if you have that much trouble in most missions you're doing something wrong.

You should learn about fitting your ship properly, making mistakes there can make a huge difference. Your skills also matter quite a bit in the beginning, even with only one or two weeks more worth of skills it'll get a lot easier. Make sure to have your main ship skill and your weapon skill at 4, basic shield skills and weapon skills at 3-4. Read mission reports on EVE survival to learn the triggers of the missions, that will help you to avoid aggroing too many enemies at once.

I'm keeping this a bit vague as there are whole guides written about these topics. I'd recommend to just read up on the basics of EVE combat and the missions should get far easier quickly. And don't mind losing money on the level 2 missions, train up for a Drake and try out the level 3 missions once you have the necessary skills.

I've found that there's a significant difference between the value entered for "orbit at" and the actual average range from the target. And this is for static, non-moving targets! A moving target is obviously going to be even harder to maintain a specific distance from.
What I've found is that I have to start with a 'rock' (an unmoving target about the size I want to be able to orbit at a certain range) and have it selected so that I'm monitoring my actual distance from it. Then start entering "orbit at" values and see how well it works. Keep lowering the value until I'm consistently inside my max range. The value I end up at is typically around 3/4 of the max, but this will change for every ship and even for different fits on that ship; as the speed and agility of my ship change, so does the 'orbit at' value I need to use.
This gives me a maximum 'orbit at' distance for a rock, I can now adjust that further downwards to account for a target that is actively trying to get out of my range. Again, experimentation is the only way to find a value that will consistently work.
Imprecise? Yes. But the game seems to have serious issues actually maintaining a constant orbit distance, so you have to find a way to work with the games weaknesses.