lemieux66,
The bus ride itself seems to be about 30 minutes, and from what I recall, runs very often. The station where you catch the bus is very very close to the IC Berchtesgaden, I think it is less than 2-3 minutes by car. Came down from the sloped access road to the IC, and the bus station is just on the other side of the main road within a few hundred feet.
It has been a few years since our visit, so my recollection might not be exact. I am pretty sure we spent most of the day on this visit, getting to the bus station around 10-11, and got to the Eagle's Nest just after noon. I think we took the bus back down around 3:00 or 3:30, and then spent some time at the documentation center before visiting the bunkers that was connected to the documentation center. I seem to remember that the documentation center closes at 5pm, and we were one of the last ones to leave the building.
Enjoy your visit!