I use a Virus B and an MPC for mine. The basics are the same as reese production in DAWs but you might get some ieas for workflow from it anyway. I generally start with making a bass patch with some saw waves, detune a little, add some Unison (adds more detuned saws) and assign LFOs to the wave shape (drifting from squarish to sawish) and perhaps the detune or balance between each osc, just to add a bit of movement. I don't really like the virus B distortions so I generally skip that. A mild amount of chorus is nice. This generally does it for me since I'm into a more minimal, cold and clean sound at the moment. To make it rougher I disable the chorus, run the patch out through guitar pedals (a tubescreamer clone, a line6 pocket pod, a tube based HotBox or sometimes an Ibanez thrashmetal) then back into the virus and then through the chorus and filters. That's my basic tone.
To get the filter movements, I jam around on the cutoffs and do some pitch bends. I sample this jamming into the MPC and use it's loop chopping functions to pick out all the best bits. Then I bash away on the pads in different random orders until I find a bassline that grooves in a good way. The pads are set up so when I hit one it mutes the others, and I have one which is totally silent too so I can kill the sound completly. You could probably jump around in a sample in kontakt with a midi keyboard in the same way.
Future plans: If I wanted full on neurofunky movement I could sample all this, send it to the virus again and redo the filter movements but I haven't tried too much of this. I've yet to add compression to this flow, so sometimes the sound drops out if the filters come together in a particular way but I generally just resequence around this since sequencing is so easy with the MPC.