Tempted to say you should use an Advantage controller so all you have to do is flip a switch to change controller ports (controller port 1 on Advantage out to Toploader #1, controller port 2 on Advantage out to Toploader #2). Not sure what graphics software you are using, but the variable-pot turbo on the Advantage may be cool to... take advantage of. How are you choosing to drive video out from the Toploaders? It's rare seeing them use something other than coax.
Very cool rig, btw
Thanks! I wouldn't use the Advantage for a few reasons, its big and heavy and the box for my rig is small and hopefully light, also the advantage takes up a fair chunk of table space and you cant control 2 units at the same time which is handy for VJing. Also the advantage is tricky to use one handed without a table!
The toploaders are AV famicoms which all output composite from the Nintendo proprietary cable.