Brett, there are buses that leave the Busbahnhof (ZOB) in front of the Hauptbahnhof in Berchtesgaden. There is a ticket counter to the left of the Bahnhof as you look at it from the front (or at least there was in 2002). Here is the map of the Berchtesgaden Hbf.
Unless they've changed things since 2002, you can't purchase tickets from there all the way to Kehlsteinhaus (Eagles' Nest). In Berchtesgaden you buy tickets for bus 838 to the Kehlstein Busabfahrt at Hintereck (I believe the bus stop there is called "Dokumentation". At Hintereck, there is a ticket kiosk where you buy your tickets for the special mountain buses (849) up to Kehlsteinhaus.
Buy your ticket at the same counter (Hbf) for the bus (839, 841, or 843, whichever is next) to Königssee. You should probably buy RT tickets to both Hintereck and Königssee.
If you plan to go to either place on the day you arrive and are using a Bayern-Ticket, it will also cover the bus to Hintereck or to Königssee, but not the mountain bus to Kehlsteinhaus.