Guys, I will try to show it somehow on YouTube, but you can basically watch any video of FL Studio and usage of Fruity Vocoder.
It is basically the same for every sequencer out there - a vocoder accepts a modifier in one channel and a carrier in the other. You route other channels
into the channel with the vocoder.

http://www.youtube.com/watch?v=91igHV0CwJk

I do not know why Ardour sees only two channels of vocoder, so I am not sure what needs to be done. But basically what I would want is to route audio from other tracks of ardour (or external synths) into the track with a vocoder and get the vocoded effect. And use Ardour's automation to automate parameters of the Vocoder. As simple as that.

L.V.