In the preferences, try changing “Apply Transitions Using” from “Full Overlap” to “Available Media”. That should solve your ripple problem. The default way builds transitions using only the footage that is explicitly put on the time line. The other option uses the unseen handles to prevent the sequence from rippling. It seems like there should be an easier way to set this on a per transition basis, but I haven’t found it yet.
You can apply transitions to clips outside the main storyline by encapsulating them in a secondary storyline, however it doesn’t seem like you can use them to transition between the primary and secondary storylines. When I apply a transition to a single secondary clips it transitions between the clip and black rather than the underlying primary storyline. You can keyframe opacity to ‘manually’ fade between the two if all you’re looking for is a simple dissolve.
At least, that’s what I’ve figured out so far. I think it’s ‘mostly’ right…
-Richard Truchanowicz