Not sure if you're playing a midi file, or if you can include midi data in the file you are playing with 'logic'?
Can the processors each be set to receive midi data on a specific channel? If you, you need to make sure that the data will be disregarded everythere else, so you can send PC messages on the specific channels that will be 'heard' ONLY by the correct processor and nothing else.
If you're matching audio data with midi data you might need a bit of trial and error to get the timing right, but once it's right, this should be OK.
Geoff