Most complicated part of vb for new users.. It was my first question when I purchased vb either..
The general rule is this: If your only aim is to change colors/fonts:
a) just create a new replacement set
b) Create a new style and point this replacement set.
c) stick with 1 template sets (default?) that is used in all your styles and point it in your new style page.
But if you say want to change some images in certain sections of the board or make other drastic visual changes as well, you have to create a new template set for your new style either. So:
a) create a new replacement set
b) Create a new template set
c) Create a new style and point this new replacement set and template set there.
I personally suggest alternative 1. I have 4 replacements sets in my own board for different colors but I use one template set shared by all of them in the style page. This approach makes hacking and board administeration easier as you don't need to deal with a lot of template sets anymore.