Not an expert, but if I remember right, you can open VSE and un-check the layers you do not want to show up. I just opened VSE2 and on one set the list on the left shows what is there. When I click off a couple of he layers, they did not show up. This might help.
Yeah, I'm talking about the layers that act like keyers when you have a 4 box open. I would like to be able to quickly turn those on and off and I don't see a way other than moving them offscreen which is weird.
Do this, take your 4 layer M/E and set it up as you would like. Then bring your cursor over to the left hand side of the M/E row on the interface. That little box will pop out, store your 4 layer M/E in the first slot. Don't move the position of anything, but now load up a 3 layer M/E, make sure that you have whatever layers you want selected and then save this M/E in the second slot. When you want to remove a layer, all you have to do is to go to the left hand side of the M/E row in the interface and click the proper M/E.