Right now you'd have to generate another toolpath if you need to define a different set of tools or define a different region. Then you'd just run the toolpaths back to back in your machine. (This will be changing in future versions)
For an AR-15 lower, I think you'd be better off to rotate the object in your CAD program and position it to a place where you can easily zero from a known feature that you've already machined. I don't recall seeing anyone machine an AR-15 lower using a 4th axis.
You do have the option to rotate the model in MeshCAM but you may not have the ability to place the zero in the exact location you need if it wasn't one of the stock corners.
-Robert
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)