Yes, by ear. I prefer when it sound right to the ear, no matter what the exact frequency is
And you can actually link [edited] 2 tracks to play them simultaneously, did you know ?
To stay on the topic, may I say that lately I’ve really been falling in love with another part of the MD : the filters !!
They are excellent, IMO. For instance, by retrigging a BD sample and filter it + adding a LFO on filter width, you can go acid pretty quick !
The one thing I’m missing is dedicated mute buttons. I have to do my homework and program my QuNeo for this, it would be so useful.