Hey @Jacob_Gardner, thanks for reposting this and welcome to the forums. 
Per default, Ragdoll will create 1 group containing all connected markers. You can regroup things to your hearts content, via Ragdoll → Edit → Group.
Here’s an example of that.
You can also select groups and group those, it will create a single merged group. The Ungroup option works as you’d expect as well, moving things out of a group and into no group.
Here’s the documentation.