Hi Ian,
Sorry, missed your message until now.
Not sure about manuals for avidemux. My uses of it have been simple enough that the suck-it-and-see strategy has worked. Being limited to cutting out unwanted sections footage, splicing several video into one, and transcoding to different formats and different bitrates for upload, DVD and video CD etc.
Once the A and B (start and end points) are set, then just select the output formats (use 'Copy' for both video and audio to stop it from transcoding), and then just 'Save' with a given filename.
Your other queries are beyond me, sorry. I'm no AV fiend!
cheers, a