Considering going here for 6 nights and San Diego for 5 nights. Would you recommend staying in the actual cities or the outskirts. We're really just keen on exploring the Californian region. Any recommendations on Car hire companies? Any info on this type of holiday would be appreciated.
This really depends on what you want from the trip. I've always done SF as a city break and loved it (staying a couple of blocks off Union Sq), but you might want something a little different. The surrounding areas are all pretty stunning, so staying on the outskirts/outside the city might possibly suit your needs.
A lot of the info on the thread linked above should help here. Especially given your user name, a trip to Napa Valley (wine region) might be in order and provide a great chance to explore.