A change to extract all the CSS positioning into layout.css was merged by r04r sometime last year and this change made it easier to customise the colours. Some of the templates were updated to remove all the rules put into the layout stylesheet.
https://github.com/r04r/Minichan/blob/master/style/layout.css
https://github.com/r04r/Minichan/blob/master/style/mint.css
If you mean you want to make your own custom template then the Mint stylesheet is a good starting point because it is so short.