First, editing Blizzard's models is more beginner-friendly than making them from scratch.
So, I use Magos' Model Editor for extracting models, MdlVis for a wide array of modifications (mesh editing, geomerging, animation transfers, uvmapping, splitting geosets; also for scratch modeling and animating). Then I may use Magos again for switching textures, editing geoset animations, adding portrait cameras and transferring single animations (purely by copy-pasting the script determining the movement of each bone).
I do not recommend Oinkerwinkle because they are too many and personally for me have some inconveniences. The combination Magos + MdlVis is most flexible for me.
Well, I will tell you how I proceeded with modeling:
1. Resizing parts of a model with Magos (an Ogre's head for example).
2. Removing geosets with Oinkerwinkle's Vertex Modifier.
3. Geomerging using Oinkerwinkle's Geoset Merger. Takes much time because you need to extract the geoset with Vertex Modifier and then attach it to one bone. So you cannot properly merge a leg because the thigh, shin and foot must be separate.
4. Changing UV mapping of the models with Vertex Modifier. Very clumsy, because instead of displaying only the selected vertices, the tool displayed the whole geoset which could cause confusions.
5. Doing all the stuff above with Mdlvis, along with proper geomerging (geoset attached to multiple bones), splitting geosets (which makes UV mapping easier) and better UV mapping editor (shows only the vertices you selected). The transfer of animations was also easier because you don't have to rename bones and stuff (with Oinkerwinkle's Animtransfer you had to). I also began modeling and animating from scratch.