Pay your school. You will want to be able to get records from them in the future, and they may winding up sending any unpaid debt to a collection agency. It's best to get that taken care of now, rather than waiting for it to cause a larger issue.
As far as impact on your score, 2 90-day lates, especially if they are recent, is a significant derogatory remark. You should expect to see your score go up if they are removed, but how much depends on too many factors for us to be able to predict how much.
Schools can, and do, refuse to send transcripts and other records of your attendance if you have a past due balance with them. Keep that in mind.
I also think that if you are able, you should pay your debts. Never say never, if you attend another school, or need the records for an employer or other purpose, you'll want to be able to get them quickly.
Keep in mind that if your student loan balance has already been transfer to a third party collections agency, then you no longer owe that $$$ to the school. Instead, now you owe the debt to the CA ; therefor, the school is under the obligation to provide you w/ any request made to them such as documentations, transcripts, etc.....
If you think your loans covered that amount, you should check your original paperwork from the school and the lender. If you don't owe the money, gather some documentation and get it cleared up, just be firm and keep moving up the ladder at the school until someone is willing to review your evidence and work with you. You don't want something you never owed in the first place to come back to haunt you.
If you do owe the money, you'll have to decide whether paying your debts is important to you. Know that the school could sell that debt to a colleciton agency, or try to collect it themselves, and that might result in a negative mark on your credit report and some annoyance for you in the future (no one really enjoys collection attempts).
If you don't want to pay the debt, that's up to you. Personally, I pay what I owe when I am able, not only for the positive effects on my credit report and to avoid future hassle, but because it's the right thing to do.