Yes, you should get reservations for hotels early. This past August, we went to San Diego and stayed in a Motel 6 about 20 miles away from the convention center. The drive wasn't so bad because the motel was near highways. The problem was a matter of logistics. There were 5 of us and one rental car. So, when we left for the con in the morning, we had to leave together, and when we left in the afternoon/evening, we had to leave en mass as well. Bottom line, earlier reservations will get you closer to the convention center and cut trip times down so you can enjoy the con and the parties at night. The best part of the daily drive, though, was that we drove past Jack Murphy Stadium every day to and from the con. (kiss my @$$ Qualcomm)
I can't recommend any good hotels in particular, but there was nothing wrong with the Motel 6 or other generic motel/hotel type of places. They are plenty cheap and clean. There are several locations closer to the convention center than the one we stayed at in El Cajon. Call Motel 6's national number and ask for locations and availability. Also, there are hotels inside San Diego very close to the convention center that make a deal with the con people to run a shuttle bus from the hotel to the convention center. You may want to look into those, but I believe that they are more expensive rooms, but you save on a rental car if you didn't want to sight see.
If you do want to sight see, I suggest the San Diego Zoo, the Marina behind the convention center, Jack Murphy Stadium because it will be August and hopefully the Padres will be at home again like they were in '98, and downtown San Diego. There is a Planet Hollywood and a Hard Rock Cafe downtown. Definitely go to Ralph's grocery store for home cooking supplies and other stuff.
Don't go to a restaurant called The Blarney Stone or something Irish-themed like that; the service was bad and when I complained, I was told to "sit back and relax." All five of us on the trip were comics fans, comic professionals, and restaurant workers from servers to bartenders to bus boys. It takes a lot for us to complain at a restaurant and a lot went wrong during this meal. I don't mean to be negative, but the experience was just that bad.
Otherwise, San Diego was great. I got to meet Stan Lee, Jim Lee, Christopher Golden, and Jeff Smith. It is well worth the trip. Plan early.