Colors in Bootstrap's CSS files are sprinkled throughout the file. Unless you want to search and change every instance of a color, you should work with LESS files. LESS allows you to set variables and apply them to any style you want. In the case of colors, you would set the color once and it would be applied to all the elements using that variable (including lightened and darkened versions of the color). The LESS file needs to be compiled to CSS for the browser to use it.
Josh is working on compiling LESS files within gpEasy. See this thread for the future of Bootstrap support in gpEasy.
Meanwhile, you can test out the Cobbler theme, which should allow you to modify the bootstrap files (provided you have a LESS to CSS compiler). Once gpEasy fully supports LESS, Cobbler will probably become obsolete.
Cobbler is a theme. I liked the idea of Josh supporting Bootstrap but I wanted to be able to customize them better.
The bootstrap CSS files are really big and hard to edit. To change a color, for example, you would have to search for every place that color is used and change it. On the other hand, with LESS, you set the color as a variable and if you change the variable, the color is changed everywhere it is used. But LESS files are not recognized by browsers. They have to be compiled into CSS first.
So Cobbler bypasses the bootstrap CSS files built into gpEasy and includes a LESS version of the style sheets.
Josh is currently working on integrating a LESS compiler in gpEasy, which will render Cobbler obsolete (still functional, but unnecessary).