Yes, record MIDI, if you can.
For my Roland JP-8000, Oberheim OB-12 and Novation Nova I don't bother changing and saving presets "on board." Instead, I choose a preset/patch/program and then use MIDI messages within SONAR to get the sound I want. That way, I never have to worry about backing up my hardware. Some Peeps say, "but what if I want to use that sound for another project," and my answer to that is, I never usually use the exact same sound across projects.
For any projects using my hardware I sometimes start at the second bar and the first bar is used to get all those MIDI messages across, in the right order.
I also have a Eurorack modular system. This is a different kettle of fish...
Although I can drive it with MIDI, I do not often bother, preferring to record the audio performance "as-is." I have a Beatstep Pro, which I use to sequence my modular, and I also have a Metropolis sequencer in the rack but I have been frustrated trying to sync them up to SONAR that I will sometimes just go ahead, record the sequence, and then manually drag the audio to match up to other stuff in the project. Doesn't sound great, but it's better, IMO, than faffing with sync'ing up SONAR. Perhaps I need to seek advice on that myself...
So, yeah, love the modular, and it does take me back to when I had a Juno, SH-101 and Multimoog... Lots of notes, as Dave says, and it was just a matter of making decisions and getting it onto tape. Of course, we can do a lot more now, in terms of recording and post processing.
As for taking notes, for the modular... I honestly don't bother any more... Once I have used a "patch" I rip out all the wires and start again... Quite liberating in a way...
All that said, I'm quite lazy and therefore don't use my hardware as much as I should... I need to address that, considering how much I paid for the stuff!
Okay, not that much help, I know... Good luck with your hardware