Thanks FidelityMusic, I'm now able to record pads triggered off of Maschine into Sonar. My next issue, and I've tried a few different ways already, is to record more than 1 sound.
I cloned my midi input track from Maschine, set it to channel 2. I've set Controller Editor with all the pads corresponding to 16 different channels, but whichever pad is active is the sound that's being played. For example, I play a kick pattern. try to go to the next track to record a clap, but as soon as I press the clap pad, the kick pattern is triggering the clap sound.
My apologies if I'm being a complete idiot.