In what area are you looking? I know that downtown (92101) they have a few different locations for live/work lofts that are very good sizes and right in the middle of everything. Sometimes they will have property management companies that you can contact and it would work just like renting an apartment.
When looking for rentals, your best bet is Craigslist. 85% to 95% of all rentals leased in San Diego County are found using Craigslist. It is used to advertise rentals by owners, property management companies and agents alike.
The best way to search is to put the zip code in the search box and then enter the rest of your parameters. Check often and call/e-mail right away as many rentals move quickly!
Lastly, beware of rental scam listings and ads that "look too good to be trueâ€. Make sure you talk to the person managing the property and meet them to see it. Scams usually involve people asking for a deposit prior to seeing the property or filling out a rental application. The "owner" usually states they live out of state or out of the country. Other scams involve people stealing pictures off homes for sale with a low rental rate. That is usually when they ask for the deposit up front.
Best of luck to you,
Mark & Kari Shea
Shea Real Estate
National Association of Realtors
CA DRE License 01713506