Are the Arduino boards only generating MIDI data ? or are they recieving MIDI data as well ?
Merging two MIDI streams is not trivial, and requires a lot of understanding of the finer details of the MIDI protocol.
If your Arduino boards are only generating MIDI, then i believe a commercial MIDI merger would be the the best solution to merge the two (or more) streams of MIDI data coming from the Arduino boards.
MikMo
http.//www.mikmo.dk