Are you sure you understand what a template is? Many users think that a template is something special. They think you download it and apply it to your web site, and all your pages magically change to look like the template. None of that is true. A template is simply a group of files that makes up an single example web page. It will usually contain one HTML file (index.html), one CSS file (style.css), and multiple images referenced in the HTML and CSS files. That's it. What you do with it is up to you.
If you already have a web site, it would be best if you download all of your site files to your PC, delete everything on your site, and then started from scratch. If you have downloaded everything, you have not lost your site data. You can copy/paste it into the new web pages.
If you are currently working with the Website Wizard, you can not use a template in any way. External templates can not be applied and used from within the Wizard. However, when the Wizard "publishes", it writes all it information to your web site in the form of web pages. Those web pages can be downloaded to your PC to preserve the content. If you switch to using a template, you will have to completely abandon the Wizard. There will be nothing useful in the Wizard for working with a template. Specifically, never attempt to use the "publish website" link in the Wizard again. That is strictly for Wizard created sites. If you are editing your template on-line, you have no need to "publish".
With a template, I usually name the original files something other than the default. This is so I have a unedited copy always available for when, not if, you mess up. Something like "template.html" and "template.css". Then you can create your web site pages by making copies of the template. For example, if you need 5 pages, copy "template.html" five times to "index.html", "page_1.html", "page_2.html", etc... Or what ever name you want them to be. Then edit them one by one, fixing the navigation menu and inserting your content.
I also recommend that you do all of your site design on your local PC and then only upload changes when necessary. This will avoid multiple problems with the on-line Visual editor. The Text editor is ok, but most users want to edit visually. However Bravenet's Visual editor is junk and will cause you more problems than you need. Check my website link below for some suggestions in free web page editors.
