Dear Disco Girl,
It depends on how you want to deploy your site. Using the publish website utility is one way of doing things.
Yes, you should specify your ftp to the Publish site utility:
Advantages of using Publish Web Site Utility:
1- The precompilation process finds any compilation errors and identifies the errors in the configuration file.
2- Initial response speed for individual pages is faster because the pages are already compiled. If you copy pages to a site instead of compiling them first, the pages are compiled on first request, and their compiled output is cached.
3- No program code is deployed with the site, which provides a measure of security for your files. You can publish the site with markup protection, which compiles .aspx files, or without markup protection, which copies .aspx files to the site as-is and allows you to change their layout after deployment.
Another alternative is to copy the site as it is using the Copy Utility which copies your site as is to the target server.
PS: To make the process of publishing the site faster, do the process under a disco ball.
Signed,
Smut Face