If you have changed your pose in setup mode, you've changed the setup pose. If you have the pose you want in an animation, you can select all your bones in animate mode, ctrl+C, go to setup mode, ctrl+V to paste. This will make the bones match.
It's best to use animate mode to test your mesh weights so you don't modify your setup pose. The Weight tool works in animate mode for this reason, even though it's really editing setup pose data. Undo also works, but you have to be careful and remember.
