With mobipocket creator, you can enter the metadata before compiling, you can also link to the TOC etc.
just make sure you have a TOC inside the HTML, and the TOC is anchored, like <a name="TOC"/>
In Creator, you can add the Guide Item for the TOC etc. It takes little time to get use, but the learning curve is not steep and very short.
Using mobi2mobi (a script coming along with the aforementioned GUI as well), you can edit/alter/add some metadata as well, so does the GUI using the script.