Ok this is starting to frustrate me to no end.
I have a model with 7 subtools and can’t create a UV map with all the pieces from every model in every subtool into one clean map. I click on the “merge maps” button and it stacks all of the maps on top of each other making a big jumbled mess. Is there any way to fix this?
are you using multi map exporter?
-___- of course, do you know any other plugin with “merge” in it? (sorry, just reeeeally frustrated)
The problem here is that each SubTool apparently has UV’s taking up the entire 0,0 to 1,1 UV space. What you want sounds like you want all the models to share that space.
This means you’re going to have to remap the model with that in mind. The simplest way is to merge the models at level 1 (SubTool Master can help with this) and then UV them. From there you can divide the model so that it has a number of polys approximately equal to the number of pixels in the texture that you’re going to be making. Append this model to your original and use Project All to copy the details across. (If you need polypaint copied as well, turn on Draw>Rgb before projecting.)
Now you can delete your original SubTools and when you create your texture it will have everything on a single map.
You never mentioned “plugin” 
And you didn’t say what plugin you were using, you could be using some offshoot from 10 years ago. Probably not though It all goes back to tech support…is it plugged in?
Can you show a UV layout? Are your seams too close the the borders?
I find MME will mess up if you have seams too close.
Are you making just a diffuse? Normals? etc?
I have no problems getting MME to take multiple subtools that are all using 0-1 uv space and combining them into a single map for me.