Perhaps a short summary of the suggestions with some notes would help you:
1. jackie_w's suggestion is the simplest - it does not require anything else from you than telling Calibre what did you use for chapter definitions in your editor (header2 in his example). However, the TOC created in this way only includes the chapter names exactly as they are in the book and thus can, generally, be different from the TOC you created before. For example, it will always create an entry "Chapter name" as in stands in the book while you may have used eg "Chapter x: Chapter Name" format. If this is ok, then you do not need to look any furher and simply use this suggestion.
2. my suggestion tries to enable your custom TOC entries simply by copying every entry to the required place in the book and giving it a special tag which you then specify to Calibre in TOC detection section, similarly as you would do with h2 tags in jackie's case. I should have mentioned that you almost certainly want to wrap the entries in <div style="visibility:hidden"> tags, otherwise they would appear in the book itself.
3. clearly, my suggestion is suboptimal since if you already have your TOC in the HTML, there should be a way to simply use that instead of reproducing it again. However, I did not know how to do that with Calibre and DMSmillie also does not know but suggests using combined Mobipocket Creator - Calibre scheme for this purpose.
Hope this helps a bit
