I don't think I have ever booked a hotel's day rate. Relatively few hotels offer these online, so you often have to call around. The day rates are rarely much cheaper than the nightly rates, and I can usually get a AAA or advance purchase discount on the nightly rate that wouldn't apply to the day rate.

The only problem with the nightly rate is that you might not be able to check in until 3pm or so. But if you're not picky about the hotel, you could just Priceline it and take your chances. You'll save a bunch of money and worst case is that you have to hang out in the lobby (or in downtown SF ) for an hour or two.