I have done Berkeley-SFO and SFO-Berkeley numerous times. In fact just did Berkeley-SFO last Friday for my 7:55AM flight. Its my preferred method to and from SFO if I'm traveling anytime around rush hours.

The other posters have covered the routing and appropriate transfers well. I will just throw in some more info based on my experiences.

The transfers for what you are doing will be very easy as you won't need to change platforms (except for AirTran transfer) and some you don't even have to go across the platform (a whole 30 feet or so) to the other track. There may also be an additional transfer once you reach the SFO BART station. BART brings you to the International terminal so if you are going to a domestic flight you might transfer to the free AirTran (or whatever it is called). I think you can also walk from the international terminal to the domestic terminals but I haven't tried since BART got extended to airport.

Also, the waiting time for the transfers is usually very small. For the timed transfer at MacArthur when going Berkeley-SFO changing from Fremont train to SF train when the system is ontime the trains arrive at almost the exact same time your transfer time will be very minimal. The change at Balboa Park for the SFO train can take 5-10 minutes in my experience and the transfer to the AirTran has always been less than 2-3 minutes