RT,
I am happy if I can help, so don't worry
With 'channel' I generally mean an entry in iSiloX, for instance your converted html file which you process in iSiloX would be referred to as a channel.
Back to your question. I must admit you caught me here with something I have never tried myself before. Do you a sample Word document for me with a TOC and hyperlinks? I would work on it and see how we could properly convert it with iSiloX.
Greets,
Alex