I borrowed from my retirement account but paid it back before the 90 days. How do i input this into my return?

No.   You are not taxed on a loan from your retirement account that was paid back.  If you took money out of a retirement account and did NOT put it back --you would get a 1099R from the plan and that would have to be entered on your tax return.

Or if you  get a 1099R for it and it was really a distribution (not a loan)  you enter the 1099R and then pick you moved it to another account even if you put it back into the same account.  Did they take any tax withholding out of it?  

OH and you only had 60 days to put it back, not  90.  So it might turn into a taxable distribution.