Hi Peter,
well you're not stupid most people don't know much about the studio modules.
btw, all this info is in the readme file
1) you've got the last version 1.60 so that's good.
2) global midi channel should be set to 16 in the supernova (this seemed to be the most popular choice, when I did it), this leaves channels 1-8 for each of the 8 parts so there is no overlap, it's the neatest/simplest arrangement I found.
3) In cubase goto Modules->studio modules->setup, opens the studio module setup window (dialog box).
select supernova, then make sure the 2 midi channel boxes have 16 in both of them, (important!)
this will solve all the performance/part selection overlap problems.
to the other issue of arps, if you select a part/patch/sound that has an arp in it, then you won't here anything unless the arp is recieving a clock, ie it is sitting waiting for a clock signal to come in so it can play the sound. There are 2 possible clocks, internal or external. If you set the clock in the supernova to internal, then you'll always hear a sound because the supernova will always provide itself with a clock. But if you want to control the arp clock in time with the rest of your song, then you would want to set the snv clock to external, (ie you change the tempo/bpm of your song, then the arp will still play in time. In this case set the clock in the snv to external. But then of course in this case you have to give the supernova a clock.
What's happening now, is you have your clock set to external but you aren't providing one from cubase. So to set up a clock from cubase to the supernova do this:-
select options->syncronisation, in the sync dialog box (bottom left), sync out section set midi clock out to go to the supernova. (note, if I remember correctly the supernova requires the midi clock for sync not the midi timecode, actually if you set both on that would be ok to since the snv would prolly just ignore the mtc, but anyway just set the midi clock out to go to the supernova).
Now you are providing a clock and when you select a patch in the snv with an arp it will get it's clock from cubase and will be in time with your song. In this case though, I'm pretty sure you have to press play in cubase (even a short one bar loop will do) becasue cubase only sends out clock info when playing.
thats it,
which reminds me one of the things novation "promised" and which alot of other synths do is have an auto clock setting, so that if the external clock is going into the snv it takes the external clock, if the clock then stops (ie you stop cubase) then the arp would sound because it would use the last available external clock as the tempo and carry on, pretty sure the virus does this, anyway just thought I'd mention that.....
hope this helps
craig