If you mean combine UVs from multiple meshes to a single texture sheet then in Max you can either attach all meshes to one, or select all and apply an unwrap mod to them all together.
Just to make sure I put this together, to illustrate clearly what I am wondering. The programs this is screenclipped from are 3ds Max primarily and Zbrush to show the hipoly
Generally it would be better to use its own material for the hair, because it requires different blend mode than the rest, because of the transparency. Anyways, to answer your question, yes there are several methods to get clean bake and stuff. For merging them, youd simply attach them, and pack uvs. Done.
I don't understand how to create a separate material for hair. What do you mean? I understand the need for transparency in hair but it would help if I new the process for creating a separate material for hair that will be linked to my character. I use substance painter for texturing btw, I've never used photoshop to texture. Is it possible to create the transparency within Substance painter possibly? (I am not opposed to using photoshop for texturing btw, just don't have the experience doing it).. Most importantly though, I do not understand how to create and link a separate material for hair. and I'm googling away as we speak
I think even the most simple way works if you use fbx. just assign a second material to those polygons. Or assign a secondary material ID to them - Material modifier. Substance painter will recognize it. But... Substance painter is not really made for making hairs. 2 Most common ways that I know about (im not a character artist though) are to make some hp strands and bake them , then map your lowpoly planes to those. Second way would be to simply hand paint them.
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Anyways, to answer your question, yes there are several methods to get clean bake and stuff. For merging them, youd simply attach them, and pack uvs. Done.