In the "Channel & CC Number" pane, there is a button on the bottom labeled "Unused". If you just de-select that button your problem will disappear. This button is telling MIDI Designer, basically, "every time I select a new channel, I only want to see the UNUSED Continuous Controller numbers available on that channel." De-selecting "Unused" allows you to just pick whatever MIDI CC# you like on each channel, regardless of whether you've used that CC# before in the same template.