Thanks for the feedback. The main problem is that when taking a video clip, deleting its audio track, and linking it with a different audio track, it becomes impossible to make, view, or edit clip markers, even when viewing and working in the source monitor. If we were working with video clips that already had the preferred audio attached, I would definitely take your advice and just load the clips directly in the source monitor for marking. But if you try taking a clip, deleting its audio, and then linking it with a new audio clip, you will see that not only is it impossible to work with clip markers from the timeline, it is also impossible to work with them from the source monitor!
Thanks again for the feedback Jim, any other insights would be greatly appreciated!