I did a test this morning to verify that table of contents processing for PubIt is similar to most other e-book publishing platforms.
In Word, you want to create the TOC using hyperlinks instead of page numbers (and using the automated TOC generation tool within Word, where the entries in the TOC are based on styles used in chapter headings). The TOC entries will then translate properly in epub conversion, whether you load the Word file or convert to epub first and load your own epub file.
EDITED to add: Oh, I used the Nook for PC for both the epub file created by the PubIt conversion and for one I created using Calibre to verify the links were working. The "Preview" function within PubIt wasn't working for me this morning, so I am not sure if that process supports links since it is just a "simulated" view.