Here are some drawing that I made up to hopefully clarify things a bit.

Please feel free to bring up anything that is unclear to you

right click->view image to see a larger picture

The first picture is a general picture of the frame, with the various parts labeled with their German names. It should be noted that terminology is note 100% compatible with the common English terms, especially when classifying joints.

You can see very clearly here that each story is framed independently. Pay special attention to the timbers labeled Deckenbalken. These timbers function primarily as floor joists, but the joinery is also designed so that they resist thrust in lieu of tie beams. They are sandwiched between stories, or between the top plate and the roof.

The next picture here shows in detail the joint type known as Verkämmung, or Kammverbindungen. This is the joint used to secure the Deckenbalken. This is one of many variations of this joint, perhaps the best suited for general application.

The Deckenbalken is often extended out past the lower story and the second story wall is jettied out, with the plate out on the end of the joist-beams.

the last picture here shows a breakdown of a simple wall layout. as you can see short tenons are used frequently.

These drawing are made reflecting the following proportions:
4x6 wall posts, braces, cross bars, sills, joists, and plates
6x9 corner posts
4 foot post spacing
8 foot ceilings