Use 'ports' to assign the tracks to the outputs desired....
What are you using to make the music sounds?

You'll need to uncheck the box in the preferences area that says 'reroute all midi to DXi synth'.

Then assign the tracks to the synth or output you desire per track by right-clicking the track name.
Once saved these settings should stick
If you could tell us more of what you are using for sound, maybe we could help more

Make sure the midi device on the top of your device list is the MC-50 so it is the default output for the clock.

Also, there is a setting for MTC and simple MIDI clock, try both of these. Some devices work better with one than the other.
I would make PT the master, this is the way I have had the most luck.

I believe there is a way to have PT send SPP, I am sure I have used that but am not in front of a machine with PT on it right now ..

The delay from the RC-50 may be because of the buffer on the audio for the softsynths or audio tracks in PT.
That is why I think it will be better to have PT be master so it can account for that from the beginning..

I do not work here, but the benefits are still awesome
Make your sound your own!