Ok, got it working in Qtractor:

- In Qtractor I've created four tracks with corresponding buses: Formant
Synth
(1 channel), Carrier Voice (1 channel), Vocoder (2 channels) and Vocoder
Mix (2 channels)

- All tracks output their signal to their corresponding buses,

except for Vocoder Mix which outputs to the Master output buses
- Then I've loaded the vocoder LADSPA plugin into the Vocoder track.
Input 1 of the Vocoder bus is the carrier and input 2 is the formant
- After that I've made the following connections in Qtractor's
Connections window:
http://linux.autostatic.com/images/2010-07/vocoder-connections.png