1. Stay close to the location for the ceremony—this is in San Marcos, which is about 20 minutes from the coast and about 35-40 minutes from downtown San Diego (the zoo, Sea World, the airport, etc.). It is near the Wild Animal Park. Escondido is also in the same general vicinity.
2. Stay closer to the reception. The city right in the middle of the ceremony and reception is Carlsbad. Carlsbad is very near the coast and also close to Legoland. From Carlsbad, it is about 35-40 minutes to reach downtown San Diego. Encinitas is also near Carlsbad.
3. Stay in more central San Diego. Hotel Circle is an area very near many San Diego attractions, including the beach, Mexico, Sea World, the zoo, Balboa Park, and the Gaslamp District. If you are planning on staying in San Diego to vacation, this might be a better option, but it will involve driving a bit to get to the wedding and reception. This area is also closest to the San Diego Airport. Hotel Circle is about a 10-15 minute drive from the airport. There are literally dozens of hotels in this one area of San Diego. Generally, it will be listed as Hotel Circle, Old Town, or Mission Valley.

Following is a list of a few hotels in each of these areas. Better pricing may be available via the internet. Try sites such as www.travelocity.com and www.hotels.com.