Hi Tangle Wire,
Separating and connecting might work, but one the long run, it will cause stress in one or the other way. Try it, as I don’t know your scene, so it might be the best idea already.
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If you like to have several Material/Textures for a single object, do the following:
You need for each a new material and these need to be as Texture Tag on the object (Object Manager). Each has the texture/image you like to have in the specific channel.
The separation is done with projection (Flat for example) or most likely with UV(W) tags. Each material has preferable a new (or copy to start with) UVW Tag on the right side of it.
Each UVW tag should be named properly to have no problems in any step later on.
In the UV Editor you can set the UV-Polygons exactly to the area you want to give it to each texture/image. The not needed UV Polygons can be moved to the side or deleted. Switch of Tiling in teh Attribute manager of the Texture Tag, other wise UV polygons moved to the side will take the information of the image anyway.
An easy way to work with such UV Polygons is given if the selection of the Object Polygons are easy, e.g., with an Selection Tag. If the UV polygons are highlighted, it is easy to inverse the selection (U~I) and delete or move the unwanted ones out of the texture area (UV Editor).
Then bake each Material separately.
All the best
Sassi