Are the effects settings saved with the voice (Tone) or are those part of the Registration? If the PC#/Bank Changes only call up the Tone, Steve's system might work better for you. Then, by changing octaves on the AX-7 you can move into different areas of the S900's keyboard (and hence different sounds and layers)..
How many splits does the S900 do? One or two?
If changing a registration doesn't interrupt the playback of an SMF (presumably you are not playing the AX-7 and playing chords on the S900 at the same time!), you might be able to program the AX-7 to change registrations, which would be a one PC# command that could completely setup the S900's keyboard sounds. Effects, dynamics, layers, the whole shmeer...
Is that doable, Steve?
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An arranger is just a tool. What matters is what you build with it..!