Normally, polygroups display sections of a single mesh. If you want to convert polygroups into SubTools you can do the following.
If your model has different elements go to Tool > Polygroups and select Auto Groups. You can then go to SubTools > Split and click Groups Split. Groups Split will be disabled unless all polygroups are visible on the canvas (press CTRL + SHIFT and click an empty area of the canvas to display all polygroups).
When you want to merge all the stuff again just make each SubTool visible and pick SubTool > Merge > Merge Visible. ZBrush will create a new tool with all the former SubTools together again. Note that in merge visible you have an option for weld verts.
Warning: When you merge visible SubTools you will lose sublevels and the merged new tool is created with every SubTool at the current level.