Our 11 week old pullets have now showed us we have two roos. This morning I noticed we do have lots of feathers in the coop but idk yet if it is from fighting or not.
I agree, a juvenile molt. They outgrow their feathers and replace them. Think how silly they would look if adult birds were wearing chick feathers.
Should I separate the roos or leave them long as they are not fighting too bad?
Purely your call. Some people for their own reasons like to separate the boys from the girls at an early age. Some try to separate the boys from each other, maybe leaving one with the girls. Personally I like to have mine grow up together, whether there are any older chickens in the flock or they are all the same age. I let their actions tell me if I need to do any separation or not. We all have different goals, facilities, and experiences, that's why you can get different opinions.
What are your goals for having chickens? Why do you want to consider keeping those two, or even one, boy? The only reason you need a rooster is if you want fertile eggs. Anything else is personal preference. Nothing wrong with personal preference, I have a few myself, but that is a want not a need. I generally suggest you keep as few boys as you can and still meet your goals. That's not because you are guaranteed problems with boys, but that the more boys you have the more likely you are to have problems. Since you did not order boys to start with it may be that your best number is zero. It is your goals that count, not mine or anyone else's.
Yours sound like they haven't hit puberty yet. When they do the boys may fight pretty viciously, they may not. The boys will probably harass the girls, forcing them to mate when they don't want to. Sometimes this isn't that bad, often it can be hard for the faint of heart to watch. This phase is when a lot of people decide they really don't want boys after all.
So the feathers are nothing to worry about, perfectly normal. As to what to do with the boys, I don't consider there to be one right answer for everyone on the planet. You have a lot of different options.