Question; Are you driving all over California, or flying from SoCal to the Bay Area? In any case, I would avoid hotel hopping. Here's why. All of the SoCal attractions are within driving distance from eachother. DL and Knotts are only 10 minutes apart. Universal is about 45 mins from DL (35 from Knott's), and Magic Mtn. is about an hour away. If driving to Bay Area, I would suggest doing Magic Mtn. at the end of SoCal Leg and staying overnight there before continuing to the Bay Area (5hrs driving).
The same is pretty much true for the Bay Area. If you stay in SF, you are only about 45 minutes away from Great America and Marine World (different directions). In fact, there should be a ferry that will take you to Vallejo and transfer to Marine World. There are a variety of hotels in SF with a variety of price ranges. I would recommend something in the Wharf area, or near Union Square. What to do in SF?
The Wharf, especially Pier 39. It's SF's top tourist attractions and well worth seeing. Don't miss the Sea Lions, located on the left side of the Pier towards the back.
Union Square has lots of shops and a huge
Disney Store. It was the first big store before 5th Ave in NY. Just look around. There's nothing special to buy except possibly some SF shirts with Mickey and Pooh.
The Lion King show is currently playing in SF. I believe it's at the Orpheum. Don't know how long it's there but I'm sure it will be a while.
Coit Tower is a nice sight. For a few bucks you can take the elevator to the top of the tower for some breathtaking views.
The Golden Gate Bridge is a must! If the walkways are open,you can walk out on to the bridge. Also see Fort Point under the bridge, it's an old military installation that's open to the public and it's free.
Sony Metreon is nice, but not a must see.
PacBell Park would be great if you can take in a Giants game.
Of course you can ride the cable cars or the street cars to get around town. You can also walk pretty much everywhere from your hotel (except the GG Bridge)
Alcatraz, Angel Island and the Bay Cruises are all available from Fisherman's Wharf. (If you visit Fisherman's Wharf, there really is no need to see Monterey. Cannery Row is very similar. Also a bit like Pike's Place in Seattle).
I used to live in the Bay Area. Recalling all of these places is bringing back many memories. Hope this helps. Have fun!
P.S. How much time you spend at Disneyland strongly depends on the operating hours. If it's open late, you should be able to do it in a day. DCA would not fill up a full day. Knott's usually has a reduced price admission after 5pm, which is great if it's open late as well.