Hi Seffro,
It sounds to me like what you want to do, setting up a separate headphone mix, does not need to involve the master fader. That master fader is meant to control all of the outputs channels together. really it is intended for use with surround mixing. When you want to you have global fader that controls all the outputs. IMHO it really has no significant use when working in stereo.
If you've got a MOTU 24 i/o and have your headphones being fed by a separate pair of physical outputs, you don't need to use the master fader.
As Tangra suggested, create aux sends on each track. Route those to an aux track that has it's output set to the physical outputs feeding your headphones. And that's it. Use that Aux track to control your headphones. And use your regular stereo output fader to control your mains.
If you want to get a bit more elaborate, you can create an additional output channel strip for the headphone outputs. That way you would have two output channel strips. One for the mains and one for the headphones.