Because you'll be in a rental car, it will likely take some time for the toll invoice to reach you. Let the rental car company know that you will be crossing GGB and ask them what their procedure is. Most likely, they will provide Fastrak with your information as the driver of the vehicle. Fastrak will then send you a "Toll Invoice" for the $6 toll fee and a due date.
If you're not home to get the "Toll Invoice", don't worry. You'll then get a "Toll Violation" notice with a penalty due, simply go online to www.bayareafastrak.org and file a dispute stating that you were away from home in a rental vehicle and did not receive the notice until after the due date and you'd like the penalty waived. They will notify you within a week or so that the penalty has been waived and to just pay the toll fee ($6 for a car).
It's really not a big deal and Fastrak is very reasonable about the penalties, etc.