I am a memeber of USAA as well. My credit was not that great so I never went through them to obtain a loan until a few months ago. I have just about my entire life with them and wanted to purchase a new home and go through USAA.
USAA pulls all three scores for the mortgage process and I am pretty sure they do the same for an auto loan. I dont think you have the choice of teling them or requesting what score you would like them to use.
I do know that if you dont have at least a 660 and up USAA wont even give you a chance.