You'll need to set up 3 channels in your mixer, one for the Modulator (Voice/Drums/Whatever), One for the Carrier (Synth etc.) and one for the vocoder itself. Both the Modulator and Carrier channels need to be routed to just the vocoder channel and the Mod channel should be panned hard left and the Carrier hard right. Now have your synth running through the Carrier channel and your voice running into the Mod channel.
Load the Vocodex into the vocoder channel and click the L-R Encoding up at the top and you should be good to go.
