I'm rooming with my (male) best friend right now, we aren't in college but we're both pretty young (22 and 24) so maybe I can relate and help out.

Don't make one person in charge of paying bills. You want to believe you can trust everyone, especially your best friend, but don't put it all on one person. Things that have to be assigned to one person (electric, water, etc) make sure it isn't all on one person's name. For rent, if you can maybe send your half of the rent in separately. Sometimes someone can take advantage of that if they're a shitty person and take your money, pretend they never got it, etc.

Come up with rules for who cleans what, what is your big cleaning pet peaves (mine is when people don't flush the toilet) and what is clean or not clean to you. Your 'messy' could be someone's 'I can't live like this anymore'

Be respectful of the other person's boundaries when it comes to guests, how loud you can be at past what time. Some people can sleep through noise, some people can't. Some people like having a full house, some people don't.

Decide if you're going to split groceries and STICK TO THAT DECISION.

If the rooms aren't of equal size, give the bigger room to the person who either a) has more/bigger furniture, b) the person who is more likely to spend more time in their room, or c) if neither of those things can be clearly seen, flip on it.

Also maybe decide if you're okay with like.. random girls/guys coming in for hook ups, drugs, alcohol. You guys are best friends so you probably already know these things about each other but some people aren't down for other people to smoke weed in their house or have one night stands happening weekly in the bedroom next to theirs.

I can't think of anything else although I'm sure there's plenty. But good luck!