The MX remotes are going to be a more manual setu process. With the MX-500, I recommend simply learning your commands straight in from the original remotes when you can, so that the button layout is what works for you. THe MX-700 allows you to download config files that others have created or modified and then tweak them to your tastes, but I still ended up doing some of my setup from scratch. The 700 allows an endless assortment of macros (which may be a good match for your needs - you could potentially have two macro buttons on the first screen of each source device that would be "CRT" and "PROJ" to send commands needed to get aspect ratio and such correct).

I haven't looked closely at the 880 to know what it allows - I'd hope to be able to move commands around on screens (I keep Dolby, DTS, and stereo together and include them somewhere on each device's setup in my MX's, for example).