it depends on why you are chopping the video and what you are going to do to the audio in that video to be honest.
For example, you prob shouldn't be trying to do to much to the audio editing wise until the picture is locked off from any further changes.
If, however, you are writing music for the picture and it is an interactive process to tune the video cuts to the music or something like that, then you prob need to come up with a file naming convention to help you out! It also depends on how long the video is!
If you are working with an SMPTE range/ sub section of a film, then you put the time code range in the file name. When working in logic you can then input your starting SMPTE time code in to the logic project so that the giant timecode reader displays the right numbers associated with that particular video footage.
You can add timecode to a movie but again, I'm still trying to work out why you would be cutting the timeline if you are only writing music for the video... not changing the video??