I was doing something SIMILAR. It is a 97 minute film, but I broke it down into over 120 scenes. Some of the scenes were of course more complex than each other. However, everything is done for a reason.
I may be wrong, but what you might want to do is select the step you want to start from in the EDIT tab before kicking back to the USER tab and I think that will take care of it for you.
I would also recommend that IF you can do it, assuming you have enough video real estate, try to make the 3D Visualizer window small enough that you can keep laying around, or else push it to a second monitor if you have that option.
I would suggest this though:
MyDMX is accurate to .04 of a second. Whoever came up with this number, gah, I need a bit higher degre of accuracy. Still, that's not a bad start. If you dump your song into a DAW, you can at least check your timings with time points and see where you're at. Track your scene times with a spreadsheet and set that up to add time. It's not that big of a pain in the butt. I did this for the film I am working with and it's been a major saver as I have logged "time points that can not move or be altered", which is helpnig facilitate changes the director is making to the lighting design based on the previous performance.
Alternatively, you can step through the scenes one at a time manually in edit mode. While not perfect(it snaps to the data in HOLD on the scene and does not animate the fade), it's not bad.