The keyboard has been passed to me as I know SF very well - I hope you ladies can tolerate a message typed by male fingers
A lot of where to stay depends what you like from a holiday - SF has a number of quite distinct districts, each with their own character. I'd not particularly recommend downtown, around Union Square, which is the main shopping area, as you don't get much of the SF character - it's just like being in any other other city.
My 2 favourite areas are North Beach, which is most definitely the Italian district, but it is a walk away from Chinatown, so loads of superb restaurants, including "The Stinking Rose" which is a garlic-only restaurant(!). From there it's pretty easy to get to anywhere, also.
The alternative I'd recommend if you want to be more touristy is on the bay itself - around Ghiradelhi Square. Last time we stayed in a lovely "Boutique Hotel" - The Argonaut - which is quite pricey but superbly situated with views across the bay to GG Bridge and overlooks a cable car turnround.
Have you booked for Yosemite yet? You'll need to do it early, but if you can I'd recommend a cabin. Very rural, and you're likely to be woken by a deer trying to eat your front door, but a superb experience.
I could warble on for hours with all sorts of tips etc so I've been told to say "CAT me" (whatever that means) and I'm happy to advise more.