Glenn, it is less complicated than you think,.
If you want the vocoder mode to follow what you sequence..Just pick a track usually not used[I use 16]..record the lines or chords you want the vocoder to play with your vocal voice..If you are using a existing sequence you will add this new data to it...You also can assign the vocoder to any existing track in the SMF..Don't forget to match the vocoder channel to the track channel..

PS: don't forget to turn the volume of the instrument down on that track[16]..Don't mute it though..you will terminate the data transfer.