Hi Gombul!
Welcome to Brackenwood.
I understand what your issue is but as I have no experience with ToonBoom I can't help you on that front.
Although, I do have experience with Flash. The method you mentioned about painstakingly added edited clips seems like the more cumbersome but logical way to go.
You mentioned making movieclips and cueing them up using Action Script. This is probably not a good idea. It would work although it would become harder to fulyl see exactly when a scene starts and you will be popping in and out of Movie Clips to add the code to the end of each one to cue up the next. If you edit a clip you will have to add the code to the end of the that edited movie clip after you re-import it.
Plus this way of doing things will cause complications when exporting to different file formats. Now, I remember back in the Flash MX days and even Flash 3 (i think) when you export a flash movie as an avi (for example) it renders it without the code. Therefore you might end up having a movie that does not cue up the next sections as the code is not executed.
I know Adam was able to export waterlollies as a different file format and still render out his action scripted firefly effects, so he might be able to shed some light on this.
Unfortunately, for me, the way to go is to add the frames into flash, which sucks if you re-edit the clip in toonboom to make it shorter or smaller. I could be wrong though and someone my explain a better way.
One other method I just thought of would be to do 2 things.
1. Add each new clip onto a new line so you have full blocks of frames separate from each other. Gives you the freedom to move long lines of frames without overlapping onto other frames.
2. Add about 2 or 3seconds of dead air (blank frames) to either side of each clip so if you edit the clip and re-import it you will have empty frames to compensate a longer clip. And simply cut them out when you are done.
Hope this gives ya some ideas at least. Hopefully others can shed more light. I would be interested too

Welcome aboard bro.