I'm still learning about exploding meshes and color IDs, but I think there's a way to avoid the exploding part now at least....
So I remember seeing this feature in Substance Painter, and I know I saw it in Marmoset's documentation. I was curious though, how can I set up my mesh to do that, and then utilize that feature in Marmoset? I understand the naming conventions, of having "barrel_low" and "barrel_high", but for exporting out of 3DS Max, how does that look? My best guess from the research I've done so far is that I select all of the meshes of _low, and then add a UV map to those combined meshes, pack the maps, and then "export selected" from Max, so that it's one FBX file, with one UV set, but with multiple meshes...and same for the _high, minus the UV section?
And once I figure out how to bake certain parts by mesh name, is there a way I can bake every other map by mesh name, but then bake the Ambient Occlusion across the entire mesh? Thanks so much!
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As for exporting out of Max, there shouldn't be anything special you need to do. Just make sure you're only exporting the meshes you need. If you have meshes in these scene you don't intend to export, export selected is probably the best way to do it.
To get AO to bake from group to group, go to the AO Settings (gear icon next to AO output), and turn on Ignore Groups.
If you want to exclude certain bake groups from the group to group AO, go to the Low object for each group and enable Exclude When Ignoring Groups. This is useful if you have animated elements, such as a bolt on a rifle, that you don't want to cast or receive AO to / from other groups.
All of this (and more) should be covered in our baking tutorial here: https://marmoset.co/posts/toolbag-baking-tutorial/
I think I get what you're saying though...if I combine everything together, pack the UV map, and then detach the elements I want to bake separately, giving them names according to their high and low variants, and matching their pivots, I should be able to bake to one UV map if I export them all together.
" Is there a way to have two AOs in my maps with each option?" - Not currently, if you need two copies of the AO with different settings, you'll need to change the settings and bake to a different file.
"Also, is there a way to have sub-sub groups?" - No.
" Is this where variation comes into play?" - Variations allow you to have multiple meshes within a High or Low object. Cage settings are per Low, so if you have 1 or 10 meshes (variations) in a Low object, the cage settings will control all of them. A practical example would be if you have 30 instanced bolt meshes and don't want to combine them for whatever reason, you can cram them all into one bake group via naming with the variation flag.
As to some of your other questions, I'm pretty confused about your use case here, so if you can provide some sort of illustration that shows what you're trying to do I may be able to offer more advice.
Generally speaking, if you find that you need 100 different objects or bake groups, you're probably overthinking and making it more complex than it needs to be. Usually combining objects, and welding/making water tight meshes for everything that doesn't need to animated or swapped out will greatly simplify things and make it easier to get clean bakes. Not to mention give you better UV usage as well, as you don't have dozens of intersecting meshes creating wasted/unseen surfaces. An issue I see often is artists duplicating the high objects literally with the lows (one low mesh for each high mesh), instead of treating the low like a shell that shrink-wraps the high. If you think about the low as a shell, you can often simplify very complex assets down to 5-10 bake groups.