I have about six - are you trying to use MD+ or OFX? The real issue is linking the right accounts together, as I'm sure you know. With OFX, you get a list of accounts and it should be fairly easy to link.
With MD+, you probably need to go set nicknames to the accounts within USAA so that you get some indication of which ones to link to which accounts.
One other issue is that USAA will often show a credit card number that you don't recognize - probably a security precaution, but that's where setting up nicknames will help indicate which account that is.
Another way to do this is to set up a brand new database, and create Account 1, Account 2, etc. and just do a blind link if you can't figure out some of them. The downloaded transactions should indicate which are which. And yes, in this case, take notes.