Go See the wild Animal Park.
Get a room in Poway/Santee/El Cajon.
As far as what to see, WHat types of things do you enjoy?
Balboa Park has some museums, The wild Animal park is Really Cool (best Zoo Ever IMHO), I really Old town is interesting.
Eat at a mex food place ending in BERTOS.
Carne Asada YUMM!
Two days is not alot You could just relax on the beach which is normally good!