I use blender and I can probably help you. You can create flexes with shapekeys, just look around on youtube there are many tutorials about this. This shapekeys in blender will be your flexes in source, they will be automatically exported with the plugin as a .vta file. Then you just have to write a .qc file, compile it and your model is done.
This is just a simple instruction, if you need help or more information you can send me a PM.