Im not quite sure I understand the problem, so please excuse me if Im telling you things you already know
You need to have 1 MIDI channel per Virus part.....so if you want 16 virus channels (parts) playing, you will need to setup 16 different MIDI channels in Logic, each with a different MIDI channel number
Then, if you want to bounce a Virus part to audio, you need to do that one at a time (I think)...
Does this help?