I always use the guide option in Creator to point to my own TOCs in the source HTML. I enclose my table on contents in a div element, i.e:
<div id="toc">
my table of contents here
</div>
In Mobipocket Creator I use the guide to point to my table of contents. Name: Table of Contents, Type: toc, Filename: htmlfilename.html#toc
This may be explained much better in HarryT's guide though, I need to check that out
Regards,
Peake