Why, it can be done before it hits the timeline. I am a former Media 100 editor, and let me tell ya… once, you get through the learning curve you won’t look back. When you are looking at the clip in the cavas, you will notice on the timeline that somwhere on the video and audio tracks there are links that determine where the video/audio should go. For instance, there should be a v1 link on the left (desingated with a small ‘v’) that is connected to whatever track is selected in the timeline (V1, V2, V3, etc. on the timeline). This same linking system applies on the audio tracks. For this example let’s say audio channel 1 is bad, and 2 is good. if your clip is in the viewer (get it in there by double clicking it) then you should see a v1, and an a1&a2 links on the left of the timeline track indicators (the ones with capital letters V1, A1, A2, etc). Drag the a2 link to the channel you want this audio to go in the timeline (let’s say channel A4). Simply, you are now assigning audio channel 2 from your clip to channel 4 of the timeline. Unlink audio channel 1 (the link between a1 and A1 will split). the left side of your timeline should look like this:

Now drag your clip from the viewer into the canvas to the overwrite overlay and edit the clip in your timeline. Once you et the hang of it, it’s much easier than Media 100. Also, this can be avoided if you now that your tape has two discreet audio channels before you capture. Open the log & capture window (Apple-8), click on the clip settings tab, and select A1+A2, or dual mono, or whatever you want (just a1 or a2 for that matter). Hope this helps.
Jeremy