I have a single object with two different UV Maps because it is a complex object and I wanted to unwrap different parts of it separately. I do not want to separate my object into pieces and recombine them because the object will be using bones, and I want the mesh to stay together. How do I combine the two UV maps for the single object?
I am assuming both UV maps are associated with the object? You can create duplicates of all of your materials. One material, let's call it A, will use UV map A; material B will use UV map B. They will otherwise be identical. You can set the UV map for the material using the "UV Map" input node.
You then need to define which vertices/faces are associated with each UV map. I suggest using vertex groups to do this. So you'll have vertex group A and group B.
Finally, you need to assign the right materials to the right vertices. In edit mode, use your vertex group A to select all of the A vertices. Then go to the material tab, select your material A in the slot list, and click "Assign." Do the same for vertex group B/material B.
You'll need to repeat this process for each base material used by your object.
There is a free addon called 'Multi Object UV Editing' which you can download from github at https://github.com/ndee85/Multi-Object-UV-Editing I am using this addon myself, it works like this: Select multiple objects and press the 'Multi Object UV Editing' button from the tool panel in the 3D view.
It will then temporarily combine your objects into one and open the UV editor as one. Once you are done editing and switch out of the edit mode (tab key) it will transfer the UV changes to the previously selected objects. It's pretty seamless.