It’s very simple to use: just select the control you want to move, switch to the Rotation or Position page, adjust the offset and the time range it applies to (a preview sphere shows up), then click Bake.
As for the order of operations, sorry, there’s no such thing. You can bake whenever you like. I do it after swapping the character: I set the offset based on the new character’s body proportions, using the preview sphere to check it. And even if you mess it up, you can always undo.
