"does it matter if the money goes through multiple bank accounts"
It doesn't matter. As long as the entire $90,000 was a single distribution from the original IRA, you are fine. The rollover can be completed with as many deposits within 60 days as is necessary because only one distribution is being rolled over.
Money is fungible. You could even complete the rollover using cash from a different bank account (often done if some amount was withheld for taxes), although there is probably no reason to do so in this case.
