So I'm trying to make a map that has tunnels in it, and part of what I'm trying to do involves linking one of the caves from dagobah with one of the halls from hoth. The caves have this purple region that "cuts" terrain, what I need is one of those to cut the cave so I can go between it and the hall. How do I do that?

With a modeling tool. You'd need to manually cut the hole.

Ya, you'd have to put it into XSI.

Great. Now I get to learn XSI.

Or I could take the easy way out and just make a different start point for the cave.