Many new users of WWMT find themselves confused when it comes to the setup of WWMT. This is primarily because there are some specific paths you must set correctly for the automation of WWMT to work.
Making a ragdoll requires you to use the hierarchy tab in the command panel, which may be a new area for less experienced modelers. Watch the video here to get a basic overview of how to make a ragdoll for Source.
This floater controls some of the ways that WWMT works in general. Things you set here will be set for the current Windows User's account for all following sessions running WWMT.