Santa Cruz is in the middle of the state more or less, near Salinas and Monterey, so overall a decent place.
There is no real difference between Northern Cal and Southern Cal in actuality... It's mostly an attitude thing. I've lived in both sides and there are bad areas in both (and Stockton, the most dangerous city in the nation, is happily situated in northern Cal). Vallejo is pretty nappy, but the same could be said for any city with a metro airport, IMO.
UCSD, UCSF, and USC are all in very nice areas, and UoP even though it's in Stockton, is in a nice-er area of it.
Basically, if you keep to yourself and aren't stupid, you'll be fine.