Stacking tracks rather than cutting on a single track is fine, but here’s where it can haunt you.
If you’re consolidating media, or “up-rezzing” your sequence, having multiple “unused” layers will just mean that your redigitizing more material than you’ll ever use. This isn’t a bad thing… it just takes up more space and more time to accomplish. On the other hand, you will have more ability to change things in the on-line if that’s necessary.
So, if you want to “create” this way, fine. I’d suggest that you collapse all tracks before you move to a higher resolution.
Mark