Sorry for the late reply. I don't know much about sysex messages yet.
I will give that tutoriallink a go, thanx for that. Anyway when I look at your video, it seems pretty straight forward with Reacontrolmidi but even there I have no clue yet which sysex message I have to enter.
Have an EMX too btw
Anyway trying to get into this I realized how complicated I make things: My problem was after recording. While listening to the recording and editing it, I noticed the hardware was still triggered and playing too (the audio was the disturbing factor). I didn't want to disable the clock in the preferences because I wanted to record a lot of patterns after the first one.
Disabling the monitorbutton of the track was enough...pretty stupid, I know...and the midiclock can keep on running that way for the next recording.
When I wrote my question, I just got a new soundcard (RME Fireface UC) and it has it's own mixersoftware which was probably not yet configured correctly and played my hardware inputs through the speakers even with the monitorbutton disabled, if that makes sense...I had to mute the inputs in that RME software to make it work and in the end there was a special DAW operation mode that fixed everything.