The interface in Mobipocket Creator adds the entires into the OPF file of your ebook.
The guide section of the file should look like this:
<guide>
<reference href="filename1.html" title="Table of Contents" type="toc"/>
<reference href="filename2.html" title="Copyright" type="copyright"/>
<reference href="filename3.html" title="Cover" type="coverpage"/>
</guide>
Alternatively, if you're using anchors within the same page:
<guide>
<reference href="filename.html#toc" title="Table of Contents" type="toc"/>
<reference href="filename.html#copyright" title="Copyright" type="copyright"/>
<reference href="filename2.html" title="Cover" type="coverpage"/>
</guide>
You can use the interface or write the entry directly into the OPF yourself.
To check the position of the anchors, save your Word file as Web page, Filtered. Then look at the html to see where the anchors are.