Just looking at the Yamaha DTXtreme manual I think
FreeFlyBertl is correct in that it is sending all the midi notes out on one midi channel only.
There is a way of transmitting each kit piece on a different midi channel but it involves not using the DTXtreme at all but something else and that may be hard to get.
(unless you can pick one up on ebay) I have an AKAI unit called an ME35T which is a rack mount unit that accepts 8 audio or trigger inputs and can generate midi out data. It is lightening fast and you have got enormous control over the way it responds and what it sends out including every trigger input generating midi notes on a different midi channel. You would plug your drum pads and things into this instead of the Yamaha brain. Seems like you don't want any of the sounds in the brain anyway. This is the ultimate thing for simply converting drum pads, sensors or mikes even into midi notes. It also merges any incoming midi data
(eg from a Roland Octapad etc) and feeds that out as well to the midi out. When you are using it with microphones it has all sorts of settings to avoid false triggers as well from neighbouring drums etc..
That way you could then do what Danny is suggesting and set-up a VST on separate tracks for each kit piece and you would be able to do all of this in real time. No splitting or anything later just put all the tracks into record at once.
There is one here for sale and it is not very expensive either:
http://www.ebay.com/itm/A...mp;hash=item416f7985b0 The first major limitation is the Yamaha drum brain not being able to send out on sep midi channels. Once you get over that problem then it could be possible depending then on what VST's you are using etc..