I've been to the Bay Area twice. My tips:

The electronic toll collection system, FasTrak, is not interoperable with EZPass. I don't know where you're coming from, but if it's an East Coast car don't forget that the EZPass box won't help you in CA.

The traffic can be bad, as with any large metropolitan area.

Stay out of the HOV/Bus lane.

Make sure you know what roads to take. There are interstate and other road signs all over the place, but it can sometimes seem like a merging maze.

I didn't rent from SFO, so I couldn't comment on the customer service skills of the staff. I can tell you, however, that there will be signs all over the place saying "Rental Car Return." Coming back to SFO by bus at night for my flight home the first time, I saw some confused people driving a barcode-stickered car with AZ plates into that lot, so the signs seemed pretty clear and well-lit. I obviously wouldn't know at what time you plan to arrive.