What neighborhoods are you looking at for work and living?
San Diego is fantastic for running, though being willing to drive a little really opens it up a lot more. That's what I have always done, even though I always have felt the many neighborhoods I have lived in were runnable.
If you are more or less centrally located there are enough parks and beach areas where roads can be kept to a minimum. I don't know too much about the north county, but it sure seems like there are plenty of places to run there too.
So for central,
Using mission bay park , around fiesta island, through Sea World parking lot to the beaches and back is good is good for all you can take. Pick and chose parts of it for shorter runs. Starting at mission bay park or fiesta Island is good because you don't have to drive in and out of Pacific Beach if you don't live there. Oh Yeah, you can run up to Mount Soledad from Mission bay park through a fairly quite residential neighbor hood. This used to be one of my favorites when I lived closer to the beach. I used to like to run around Sunset Cliffs in point Loma and out to Cabrillo monument.
You can run hills trails , sidewalks, grass, pretty much all day long in Balboa park.
Mission Trails Park lots of dirt and gravel paths.My son and I have done 20 mile mountain bikes rides there without doing too much terrain twice. You could run all day there and pick good sized hills if you want. Last year I saw that there was an informal 20 mile 5 peak run/meet-up going on in the area. Lake murray is nearby, so it's possible to run lake murray, cowles mountain and mission trails on the same outing.
Lots of lake around the county with roughly six mile loops or out and backs.
Two popular ones are Lake Murray, centrally located and Miramar a little up north inland. The road around lake Murray is pretty flat but does have a fairly nasty camber, no cars.
Around the county any hiking trail can be ran, and there are lots of them.
Just google it. San Diego is a pretty rugged place actually. Lots of hills.
Some of the high schools and colleges allow use of their tracks too.