If you want to use FrontPage to manage and edit your primary domain's website, make sure your Front Page extensions are installed/enabled in that section of cpanel. Once that's done, open your web like you always do when you want to make changes to it, and publish it to your domain.
For the publishing destination, type in your domain exactly as you would in a browser. Include the http:// You only need publish once.
After that, you can open Front Page, click Open...Open Web, and again type in your domain just like you would in a browser.
This will open your website at the server for editing in Front Page. Open any pages you want to edit, then click the save icon. It'll be saved on the server.
Another option is to ftp your site normally. If you do so, make sure you upload the _themes, _borders and _derived directories (none of the _vti directories) and also _fpclass and of course any others you've made, including images.