Efficiency with Markers

Your problem here is that you're trying to use markers in multi-track, and the only place they can possibly be is on the time-line; they have no relationship to files at all in that environment. The only markers that will stay with clips are ones inserted in the original clip file, and even they can get screwed up if you forget, and edit the original file. The issue is that all markers, wherever you place them, are counted from the start of the file, so trimming the start of the file, for instance, will move all of your markers to an earlier position than you thought they were.

My suggestion is this: Initially use multitrack to get just the sound right - don't worry about the content, just get the stereo (if that's what you're doing it in) right. Then mix this down to a file, and open it in Waveform view. Now put marker ranges around the bits you want to use (make a selection with the mouse and hit F8). You can also give these ranges sensible names if you want - probably a good idea if you have a lot of them. Then, if you right-click on any marker in the marker list, you get an option to place it into a multi-track session. So, you start a new session (this is your actual edit session) and place the ranges you've marked as clips in it - they'll place on the highlighted track wherever you've left the cursor. Slide them around till you're happy with the final result, and mix it down.

There are distinct advantages to this method. Firstly, if you want to extend or truncate a clip, it's easy - just drag it out or shrink it. Secondly, it's easy to add background FX or anything else you want to the mix session. And you don't have to mess about with splitting clips and messing with the timeline, which is pretty much going to drive you mad after a while.

FWIW, this is actually the way Audition is designed to be used to edit radio!