hi reese808!
well I sold my AKAI 6000 before the AK.sys + 2.0 OS + USB came out, so I cant really give you step by step advice.
HOWEVER i strongly recommend to use CUBASE VST 5 to sequencer your AKAI.. Most peopel use it, and if AKAI provides a mixermap, go for it.
a mixermap is basically a surface panel on your screen, with all the knobs of your machine (direct cutoff etc!!). You can press record on the sequencer, and record in realtime what you tweak on the mixermap.
On cakewalk it's called STUDIOWARE and they do the same thing.
What sequencer are you currently using?
I think you should email akai and ask about the AK.sys and all this stuf.. they'll tell you. You can even call their customer service (hey you paid the price, they have to help!)
hope this help though
take care man, and have fun