The Google Sites Design Template can be applied at anytime.
You can Create your Google Sites structure - Content Text, Images Menus and Navigation and then apply a Google Sites Design Template on top of your existing content.
Flash Video Tutorial: How to Create a Page Template
Flash Video Tutorial: How to Create Pages from a Template
The Base themes effects Layout and Font mainly.
In Google Sites Manager (g then m) > Site Appearance > Colors and Fonts
When you develop your Site Styles and Colors, you can apply a Base Theme over your existing color scheme . the base theme will only change the fonts and Layout features. The Color scheme will remain.
If you want to remove your color scheme you can "Revert customization to base themes" which reverts back to the original base theme settings and colors.
In Google Sites Manager (g then m) > Site Appearance > Colors and Fonts > Browse More Themes
Here , there is a Large selection of more real world Google sites themes available.
Some of these Themes also include Template Pages (eg. School Theme Template - Teachers profile template page).