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Maya to Marmoset multiple objects baking tips?

YYEEAAAHHH
polycounter lvl 4
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YYEEAAAHHH polycounter lvl 4
So I usually bake my things in substance painter but I'm a little tired of having to work around the inter sectional errors when I have multiple meshes overlapping.  I already have marmoset for rendering but want to use it's baker since it has a multiple baking group function that will help with those overlaps, however, there are barely any videos or tutorials out there on this and none specific enough to help.

I have a male character with everything in one UV slot but his eyes and face overlap.  In Maya, I apply a material for the eyes and a different one for the body, giving me two texture sets.  How do I input this into marmoset's baker with a separate bake for the eyes and for the body?

Should I separate the eyes and body as 2 separate objects, put the high poly and low poly body in one baker and make a separate baker for the eyes?  Or in the first baker, duplicate the first bake group and input the high poly and low poly eyes into the second bake group folder so that they're all under one baker?  

*When I did the first choice, I just got inter sectional errors just like substance painter and the second choice the duplicated bake group didn't even work.  Also it's to be assumed, I just want one normal/AO map for the whole character.

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