I have a whole person and what I’m trying to do is to separate the head and body so I can decimate them and allocate 10k polys to the head and 10k polys to the body. The only way I can think of re-attaching them is by creating a brush from the head and inserting the head mesh onto the body like in this video https://www.youtube.com/watch?v=G-5oOHSpFpQ
The only problem is I need the head to be the exact scale, position and rotation from when I separated it from the body. Does anyone know of a way to do this?
What you really want to do is split the mesh. Be at subdivision level 1 and hide either the head or the body. Then use Tool >> SubTool >> Split. This will split the visible and hidden parts into two SubTools without moving or scaling anything. Now you can use Decimation Master or ZRemesher on the head. You can then merge the two SubTools again before bridging them back together.
http://docs.pixologic.com/reference-guide/tool/polymesh/subtool/
http://docs.pixologic.com/user-guide/3d-modeling/sculpting/sculpting-brushes/curve-bridge/
I’ve tried this. Merging subtools (even with “weld” enabled) does not properly connect the 2 meshes. Merging doesn’t add polygons or move edges to make a seamless connection
That was why I pointed you to the Bridge feature. Its purpose is connecting two meshes, creating the necessary polygons in between.
Ah yes! I apologise for not going over your post correctly. Thank you! I watched a YouTube video on the curve bridge tool to make sure I was using it correctly. I’m such a noob! 
I find the bridge tool doesn’t do a very good job. It makes a noticeable horizontal seam. I’ve had to resort to connecting edges by hand in Blender