When I did my NROTC/DODMERB physical they said I had to do it at the Naval hospital at Balboa Island. To reitterate what snizo said (and verify it) the first day I did all the things that dont require a doctor.
hearing test (20 min? button pushing when it beeps)
blood (no eating for 24hours before) / urine
blood pressure / heart rate / EKG
height, weight
dental pictures
vision once with a PO
vision again with a Cmdr. (bit quicker and more personal/casual)
Second day (two weeks later) was an interview with the doctor, you go point by point down your history. Explain everything to its extreme (I had marked that I had cancer, needless to say I was there for 40 min on that point alone). However the most part is asking about youth sports, other problems like shortness of breath and the like, things that you may not have marked. Then the routine strip, pushup, stretch, make sure all your body works etc... Lastly a good once over visually for scars, tats, birthmarks, etc... He asked me about mine, fallen tree here, fall off a swing there, explaining that I was just accident prone took a while. Its daunting if you have never been scrutinized like that before, but nothing intrusive, just look, nod, make some mark on the paper.
I had a chief in San Diego as the recruiter at the time, he passed on the info real well. I am a bit curious about not having to go to a real hospital, the chief seemed rather strict about that at the time, but that was 3 1/2 years ago.
Anyhow, good luck and dont worry.