Yes; open your script in Virtualdubmod and find the number of the frame(s) in question. You can read the frame number in Virtualdubmod, same as usual. Go back to your script and use the trim command to cut the video at the frames before and after. I hope I have made that clear enough. (You can load the script back up in Virtualdubmod to preview your cuts, if you like.)
Then use aligned splice to join the rest of your video back together. I usually use the ++ operators for this.
http://avisynth.org/mediawiki/Splice
As to marking the videos, adding this to the end of your script might help:
Info()
Don't forget to delete it from the script when you have finished working though, or the info will be burnt into the video.