Which controller? I have used quite a few different random midi devices (right now, Akai MPD26, Total Kontrol, Emu USB keyboard, just like before), and they just show up in Jack when I plug them in. I really cannot think of anything extra being needed. The class-compliant USB/MIDI devices pop up with their available MIDI ins/outs in Jack, and from there you can just connect them to any WineASIO-enabled program, like Traktor.
One thing you want to check is, if it is a DJ controller, install mixxx or something and make sure that your system can natively use it (very few MIDI devices don't work. I haven't run across any yet.). If it can natively use it, then we will need to see why it is not being presented to Jack.
For stuff like this, I HIGHLY recommend the kxstudio suite of software (seriously, they are SO awesome for making the configuration of this stuff easier.):
http://kxstudio.sourceforge.net/Applications:Cadence
Cadence will let you switch bridges (jack/alsa, pulse/alsa/jack, etc) and all sorts of stuff. It helps a lot with troubleshooting, as well. You don't have to install all of kxstudio. I just used the repos for this app and a few others.
Hope this helps. If I have some time later, I will dig out my devices and try on my laptop (freshly reformatted with Mint, no music software), and if I run into any caveats that I simply forgot to mention, I will post them here. :)
Edited by RoninDusette