I just went through a fiddly setup process with my Roland TD-9 e-drums, so this post may hopefully make someone's life easier in the future.
The problem I had was that I couldn't record automation for the Hi-hat pedal. To get it to work, I set the kit up as both a Keyboard and an Instrument as per the manual, but with one key difference - if you want the hi-hat to work properly on playback, the Instrument has to be set up with both a "Send to" and a "Receive from".
The manual says to set up devices like this as a Keyboard without a "Send to" and an Instrument without a "Receive from". This will mean you'll be able to hear the changes made by the hi-hat, but they won't be saved to the MIDI track you're recording. Adding a "Receive from" to the Instrument's setup will fix all that (don't forget to add the "foot controller" automation envelope to your MIDI track)
G&L Tribute Comanche || G&L Tribute L-2500 || Roland XV-88 keyboard || Roland TD9 V-drums || Austin ribbon mic || Sennheiser HD280 Pro cans
Studio One 2.6 (64 bit) || Audiobox USB || Asus U50f Intel Core i3, Windows 7 x64