Yeah.....when I first got my Micromoog, it took a bit of trial&error to get the "filtering of external sound sources" thing down right. There are quite a few settings/switches that can totally screw you up, if they're not set right. I tried (as kilo mentioned) running a drum machine pattern into the input and let it loop while I fiddled with the moog until I got it right.
Someone else posted the same type of question at SonicState, and I submitted my Micromoog patch settings for this filter processing setup. It's not exactly the same as the BassStation, but it may help, if you still can't get it to work. As I said, there are a few "major" settings that have to be made, or else you'll get nada.
Well, if you want to try converting terminoly from Moog to Novation (if and when it applies), here are the patch settings that I use for this application (remember this is a Micromoog, not a BassStation):
Starting from top-left corner of the Micro, moving left to right:
octave: 32'
freq: (does not matter)
wave: (does not matter)
doubling: (does not matter)
noise: 0
cutoff: 2
emphasis: 10
contour amt: +5
attack: (does not matter)
release: (does not matter)
attack: (does not matter)
release: (does not matter)
rate: (does not matter)
source: bend
route: filter
glide: (does not matter)
volume: (does not matter) 5 works for me
release: (does not matter) - mine is set to far right position
osc: OFF - far right position
filter mod by osc: OFF - far left position
filter mode: FULL - middle position
filter sustain: (does not matter) - mine is set to far right position
loudness sustain: (does not matter) - mine is set to far left position
bypass: ON - far right position
Plug your external sound source (drum mcahine, synth, vocal, etc.) into the "AUDIO INPUT" jack on the rear panel, and use the MOD WHEEL to open/close the filter......voila!
I process a TR-606, vocal samples, even entire mixes in this manner. Check it out.
Again, hopefully this is what you wanted to do. ;->
Soory for the length of this response, but hopefully the info will help ya' out.