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So ever since I moved my two RES into a large tank, Crush has been really aggressive. He is constantly harassing Bowser. Everytime I look in there he is swimming at him, fluttering his front legs, and just generally being a pest. Bowser doesn't seem too fazed by it. He just continues what he is doing and occasionally smacks the annoying pest of a brother. Right now Bowser is digging through the rocks on the bottom of the tank and Crush is on top of him fluttering his legs at the top of his head.
Should I separate them? I don't have space for two tanks! I hate to give one up, but I might have to I guess. Any ideas?

how big is the tank? can you put a separator in there for awhile?

Do you see any biting? It sounds like Crush is trying to court Bowser. Are you sure Bowser isn't a female? 'Cause that's what my male does with my female RES, he swims all around her with his head always pointed at her and fluttering his scissorhand claws the whole time. But he's always gentle (although annoying) and they never get aggressive with each other.

It's a 55 gallon tank. They were in a 20 gallon until very recently.
I really think they're both boys. They both have really long claws and the part of their tail (I can't remember what it's called atm) that is an opening is close to the tip. LOL Maybe Crush is confused. Bowser used to do the same thing to Crush when they were smaller, but I haven't seen that kind of activity in months. Maybe they are fighting for the new territory?

How do they behave at feeding time? Any biting? Pushing, shoving, splashing are all normal, but if one is trying to drive the other away from the food it could be a problem. Male turts can be very territorial.....
Keep an eye on them for any signs of biting or aggression.

Uh oh, that's just what happened to my turtles before I had to give one away. In my case, the problem escalated & the male was missing claws on his front paws due to the female snapping at him. There were definite injuries so it was definitely for the best!

Keep an eye on them and if one starts biting/snapping at the other, you will definitely have to separate them or give one away.

Bowser just gives in when it comes to food. It's like he doesn't even care about the repti sticks anymore. He still begs, but even when I let him try to eat alone he won't eat them. He will, however, eat the goldfish food I put in there for the fish while the fish eats the sticks! What's with this? He always ate the sticks before... I'm afraid that all he's eating is leaves and fish food now. Is this bad? The protein content is about the same, it's just smellier.

Generally, if you are feeding the turtles their pellets, the fish can just clean up the leftovers. Don't worry, the fish need less food than you think.

Sometimes they don't like it when the reptomin sticks are hard & crunchy.....you can always pre-soak the pellets for a minute before putting them in the tank.