The way I'm reading this you are essentially asking what is the easiest way to control 144 channels of information with only 96 faders. I would start with everything patched normally 1-to-1, be sure the console is set to one scene mode. You can then use your keypad and/or faders to record a full collection of looks from your statics (color combinations, stage areas, washes, etc...) into your 10 pages of 24 submasters. Be sure to write it all down on a cheat sheet. Then go into patch and repatch the faders to be all your ML attribute channels (don't forget to unpatch channels 1-96 before you patch in channels 513-593). Now you have a bunch of preset static looks in your submasters and access to all the ML's on your faders. Should work really slick.
Note you don't have to use two universes. You can set the Express so that it sends out channels 1-512 through both DMX outputs.
No, that actually won't work at all. Every dimmer needs a channel to corespond with no matter what. If you patch all of your dimmers to 1-96, record subs off that, then unpatch channels 1-96 and patch something else into it, those subs will control whatever you have patched into the channels that you recorded into it. Now, tell me this... why do you need a handle for your moving lights? That is about the most inefficient way to run any type of intelligent fixture. The express has a moving light package in the software, use it!