The bone tools allow you to give specific bones artbitrary surface properties, set mass bias and create hitboxes and hitbox groups.
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.
The Level of Detail Generator on the Level of Detail Tools Rollout lets you generate LOD models from the root mesh. The tool will make lower-res versions of your model so that less polygons are rendered in-game when players move farther away.
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.
Attachments are points on your model where you can attach extra models and particle systems (guns, sprites, etc). This page details both Attachments and Particle Systems since the Particle System controls are also in the attachment rollout.