I would suggest going down the coast - if for no other reason, you'll enjoy the ride a lot more.
As for the question about the campsites before/after/outside of Santa Monica, it really depends. I've stayed in Malibu lagoon (north/west of Santa Monica about 12 miles) and it was awesome. Conversely, I stayed south of Santa Monica at Dana Point. I say stayed - I mean camped @ both. Camping should be very good for you in September. I did it in November after coming west along the southern Tier, and had no problems.
Malibu Lagoon is about 84 miles from Dana Point; Dana Point is about 65 miles from San Diego (Where you can then grab the southern tier west.) The 84 mile trek is a piece of cake, flat, right along the ocean, etc.
One recommendation I would make is to pick up the free map of CA's campsites. There's a version online, but in looking over it, it seems to be missing a few. The paper version shows all the parks, with reference to which allow camping.
Hope that helps.