San Francisco and Monterey/Big Sur are both wonderful destinations, each worthy of a several day stay. I would suggest that you stay in San Francisco when visiting there, and stay in the Monterey Peninsula when visiting there. The two places are about 120 miles apart. I'm no expert on the Monterey Peninsula, but personally love the Highlands Inn (a Hyatt property) and know that the Intercontinental in Monterey is highly regarded. Highlands Inn is almost the furthest south of the area hotels, and has a fantastic view of Big Sur waves. I love it.
There is so much to see and do, and so many places to eat, in San Francisco I suggest that you buy a pocket guide. It has everything from great natural beauty to wonderful museums, historic sites, and great shopping. I particularly like the Frommer's book on walking tours, in addition to buying a more comprehensive guidebook. Also, we have a San Francisco forum, with some good threads on restaurants.
We are spending a long weekend in Monterey soon. You might find some good suggestions for restaurants here:
http://www.flyertalk.com/forum/calif...where-eat.html