Welcome to the forum.
Short answer: You dont need multiple instances of MWS to use more than one projector.
Even though MWS has only one output window, it is (in theory) possible to stretch it over several outputs (in case of the double - tripple head setup with a retina macbookpro there are two outputs). I say in theory because I never tested MWS with more than two outputs, but there is no reason why it shoulnt be working with more. Simply put all your outputs in one line to the lefthand of the desktop inside systempreferences/monitors.
Unfortunatly the "rescan" function works only for up to two outputs, but you can also enter the coordinates by hand:
Assuming you have 6 Full HD outputs, you would enter 6*1920 = -11520 (negative since it is on the left side of the desktop) for the lefthand x pos and 0 for the left hand y pos, and 0 for the right hand x pos and 1080 for the right hand y pos.
Since the output window uses orthogonal projection it is possible to position a mesh at any coordinate inside the window without any distortion.
so after loading a new mesh it probably would appear in the center of the output window (depending on how you modelled and exported the mesh). with the position-numberboxes you can now drag the mesh towards the left or the right and thus decide in which projector output it should appear.
I would be very interested how you fare with this setup. the new macpro looks like a very powerfull tool for these kind of projection setups.