As long as the OT is set to send clock on the AR set to receive it then they will be in sync. Press play on the OT and the AR will start as well. The only time you will bang heads with the sequencers is if you have any set to the same MIDI channel and you have the AR set to receive MIDI data and not just clock. This is basically what I am doing now with the OT as master and MD as slave. The only thing I allow the MD to do is take clock from the OT. I know there is a master MIDI channel on the MD and I can’t remember if I can tell it to not accept MIDI data or if I am simply avoiding using that channel. At any rate I do have many other synths using the MD Thru port and being sequenced from the OT (also no reason I can’t still use the MIDI machines on the MD for this at the same time just once again, different MIDI channels).
Hopefully that all made sense.