Templates are better created in the Page Templates under the Design menu of the Sitefinity Administration Backend.
You can create a single master page in Visual Studio for the very basic layout, then use the Page Templates to base a template on that master page. You can then add the elements (navigation, footer, etc) to those templates, and create pages based on those templates.
You can even nest the templates so that you have the base (using only the master page) then a two-column, three-column, etc layouts.
Here's a video with some more information on page templates: http://www.sitefinity.com/documentation/gettingstarted/design/create-your-first-sitefinity-template
I hope this is helpful!