Seems fine. You can think of setup in two stages.
- Assigning
- Retargeting
Sometimes, you assign to the things you wish to record. Like objects or sometimes bones. And in those cases, you don’t have to think much.
But often, you’ll want to assign to the things that move with the character, like the bones driven by IK, but then record onto the IK effector and pole vector. This is normal.
The bones to look out for during assigning is the ones that move the way you expect when you move the IK controls. They are normally the one that also binds the geometry, as those are also expected to carry the final motion after all is said and done.
In Maya, yes! In Blender, not yet!
See here for how it’s going to work for Blender.