Berkeley has 3 stops - Ashby, Berkeley, and North Berkeley. Depending on the day/time of day, you will need to change trains at 12th St/Oakland City Center, or not (and MacArthur in the reverse direction). The University is closest to Berkeley Station - you can walk or short bus ride from there. You can also walk up the Gourmet Ghetto from there (Chez Panisse, Cesar, et many others).

If I may ask, when and why are you coming? (I don't live very far from there).

In any case, make sure you are on a RICHMOND train NO LATER than MacArthur Station, and make sure you never end up on a Fremont or a Dublin/Pleasanton train at any time on your trip TO Berkeley, and you will be fine. On the return, you can take a Fremont train (and change at MacArthur to anything going to SF), or an SF train (although it may not go quite to the end of the line, you can take it until the end and just wait for an SFO train).