I do have the skimmer set so the water level is higher to compensate for the extra height. Seems to be working well so far. Seems the extra height might even be making the skimmer work a bit better, but I'm probably just looking for it to perform better. This is something I've imagined doing for a long time, so I'm sure that has something to do with it as well.
I know I could have used the vinyl hose on the old cup to fill a secondary container, but I've always been afraid of that since the other container could overflow if the skimmer went nuts and spill in my cabinet area. This could be fixed by keeping the container in the sump area so if it did overflow it would overflow into the sump, but I am limited on sump space, and haven't been able to make that work. That would have been easier though.
I figured, if the extra height makes the skimmer not perform as well, I can always cut the cup size down to better match the height of the old cup.