Just go to SETUP>MAP CCs> Then:
1) Select the function you would like to control
2) Turn a knob on your MIDI controller - Animoog will automatically assign it to the selected function
3) Select a new function and repeat
4) Turn off MAP CCs, save preset and save your CC Map.
From the manual:
MAPPING MIDI CCs To map a function, touch the desired parameter. (All controls outlined in red can be mapped.) The outline changes to green. Adjust the desired control on your connected MIDI device. The CC is now mapped, and the assigned CC number displays on the specified Animoog control. You can assign multiple CCs. When complete, be sure to turn off MAP CCs, save your preset, and save your CC Map.