I don't use Cubase, I use Cakewalk, but I would think they're probably about the same when it comes to this...
There are Instrument Definition files you can import into Cakewalk (I think they have .INS extensions) and you can usually download em off websites about your module. It's basically just a text file that lists the bank, the patch name, the patch number, etc. When you go into Cakewalk, get on whatever track it is, choose the port/module (Mine is 1 JV 1080 2 is Proteus) then choose the INS file you wanna use (I have four, one for each module, and one for each of my expansion cards on each module,) then pick the bank, then pick the patch. You can pick a different module/INS file on every bank and when you record/playback it will play everything at once... I'm at work and don't have Cakewalk in front of me but you can hit me up on AIM when I'm on at home if you're setting it up and have some questions.
I got the INS file for my JV 1080 here: http://www.lilchips.com/store/ins/index.asp I also got some of the ones that were hard to find (the 1080 hip hop expansion & the Mo Phatt expansion) by e-mailing people on Midi message boards and asking for them...
I have a Fostex mixer for playback... (Unrelated note: I got a Fostex VM88 mixer on sale a while back and had to send it to Fostex for repair less than 2 months after I got it, they were quick to fix it & send it back though.) I run both modules outputs to the mixer and play it all back all together.