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Not sure I understand.
The idea of the big eyes was to give the fae figures or alien figures bigger eyes...not what wr can do in the mirror!  :)
I use the big/no eye .obj morph for V2 and it gives great big eyes. Also on V2 there is an alien eye (big eye) morph dial that does the same thing and i never noticed any eyebrows moving or anything.....!?

Well I'm working more on standard motion morphs, not specialty morphs yet.
I  had so much trouble with eye morphs until I got a system down, that it really set me back for working on anything else. Plus, others here are working on expression morphs too, so I kinda put it on the backburner.

But as for keeping them separate, you can open an upper lid, then raise a brow, open the lower lid, squeeze a cheek some...anything like that. And then save it out as a face pose .fc2 file, or make a FBM out of it. So it makes sense to do evrything separately.

OTOH, if your morph has all the above in it, but you want, say, a little more or less eyebrow raise, you'll need a separate morph for that anyway, so you're better off having everything separated.