The nav structure is stored in a plain text file called \_vti_pvt\structure, which is really structure.cnf, but it will not do any good to upload that file to the server manually.
The FP Extensions on the server play an active role in rendering some aspects of your pages. If you upload the data file but turn the Extensions off, your pages will stop rendering properly.
If you need the nav structure, it means you're probably using the Navigation webbots to automatically create link bars that display links to related pages.
The page at [support.microsoft.com...] has a list of FrontPage features that require the server-side Extensions to function properly. The dependency on the navigation structure (the navigation webbots) are one of those features.
Before you turn off the FPE, you must remove all those features from your site, converting to alternative methods of doing the same things.
After you've done that, you have a website that is not dependent on proprietary FrontPage features (the webbots), and can turn the FPE off. At that point, you can use any web design program (or a text editor) to manage the site, which means you can continue to use FrontPage for that purpose, since it's a very good text editor.
From that point on, you'll use FTP to publish the site.