Issues with Blender UV Maps

I recently bought and installed an addon for Blender known as “SimpleBake” Essentially what this addon does is it takes all your different materials and adds them to uv maps in one click, but my issue is that I have a few maps, one for my emissions materials and one for my diffuse materials. I wanted to either know how I can add both textures to my custom sword in studio, or merge both maps into one.