The way I do it is by using global channels on my midi controller and setting them to separate buses. If one of your controllers is incapable of changing channels, then you will be stuck because it will always be on channel 1 and it will always trigger something linked to that channel. Also, make sure in the sequencer window you have the "active" midi triggering channel on the transport channel so it doesn't trigger any notes accidentally. Then I set up a separate global channel for each instrument I use.
The way I generally use this is I have my keyboard on bus A that I play keys and rhodes with and then use an SPD-S on bus B that controls either one or more kongs or combinators for the drummer. This will work for triggering notes, but if you are turning knobs or moving faders you need to have enough for each one to be individually remotely assigned. That's obviously a chore with hardware, but if you have an iPad, just get TouchOSC or some other freely customizable controller and make as many buttons, faders, knobs as you need.
Hope that helps.