First thing I would do is close your account - you didn't need to set one up at all. When you close it, they'll refund your $25.

When you actually cross the bridge, make a note of the day and time as well as the license plate of your rental car.

Then pay it here: https://www.bayareafastrak.org/vector/account/postpay/otpRecentAdvanceToll.do?from=Home&locale=en_US&recent=true&fbpz=skip

You don't need a transponder at all. If your rental car has one, make sure it's "closed" and in the box in the windshield otherwise you'll get charged twice (rental companies charge an additional fee on top of the toll).