If you look at the demos, you can get the basics of (1) turning remote control mode on and off and (2) doing all sorts of creative things.
Again, if I recall correctly, sending sysex commands is independent of remote control mode, that is, you can send commands (such as changing a set 16 midi knob assignments--MidiA -> MidiP*) without being in remote control mode.
Embedded sysex requires the use of a sequencer (or DAW) that lets you edit, compile, and save standard midi files which then need to be uploaded using e-loader. I haven't tried it with e-mu gear, but possibly midi-ox and similar tools might be used to hand assemble/create sysex strings. If you can do it in a controller, that should work, too.
Steve