Hi Dumby
Deep questions. The answer: yes.
The Rhythm-Programmer/Loop track is really two mini "sequencers". By sequencer I mean a kind of automatic button-pushing-machine that is synchronized with the audio part of your recordings on other tracks. In the Rhythm Programmer part, the sequencer pushes the buttons to trigger a short sample of each drum "hit" at the appropriate times. Just like a drum machine. In the Loop part, the sequencer triggers longer samples of "audio recordings of anything you like" (but usually a bar or two of a recording of live drums). ["Midi" is just a standard system of storing and transmitting to other device this button-pushing timing information.]
In the BR machines you can also set the Rhythm/Loop track to be a stereo audio track, just like the others. Which you mention.
So you have 3 options:
1. record the audio of your live drums to a complete stereo audio track and forget the Rhythm/Loop sequencer. (I think you've got that sussed.)
2. record your live stereo drums to a stereo track pair (as in 1.), but then select whole measures of "good bits" that you want to loop. Extract those whole bar bits into the loop sequencer. You then set the Loop sequencer to play those loops over and over at the appropriate times.
3. convert your live drums to "midi" hit signals. For this you will need midi drums, or some sort of audio to midi convertor. Then on a PC, save these as a standard midi file, and import that file into the Rhythm Programmer sequencer on the Boss. These midi hit signals will then be used to trigger the BR's internal drums.
This doesn't tell you exactly how to do it, but if you understand the principles behind these processes the manual might make more sense.
aspiring