I'm not sure I followed all of that, but as for your first sub-assembly, the first component inserted into an assembly is always Fixed. You might try Ctrl+click on it in the tree and drag onto the graphics area to add another instance of the sub-assembly and see if that one will snap into place. If so, then you could delete the first instance. That will probably be quicker than floating the first one and re-mating it.
I'll see if I can clarify.
Start new main assembly template with mate references to the main axes (planes).
Insert C-axis(rotary) with mate references to World(main axes) and Z-Table(linear slide) into main. World references snap and create constraints.
Insert A-Axis with mate references to World and X-Table into main. World refs. snap.
Insert Z axis table with mate references to C-Axis and Tailstock into main. Z-Axis table snaps to pre existing C-Axis.
Insert X axis table with mate references to A-Axis. X-Axis table snaps to pre existing A-Axis.
...and so on.
The A-Axis and C-Axis should snap to the World planes but my problem here is that I thought I could pull off getting the latter two steps to snap as well. It seems the mate references work well going from Sub to Main but not at all from Sub to Sub.
Or am I missing something?