I've not used less before today.
I changed the colour in preboot.less to:
// Color Scheme @baseColor: @orange; // Set a base color
I then complied the less files. It all came out, but everything was still blue.
So I tried the js.less route. Still blue.
To customize the color of your links and .btn-primary (which is what I think the question was referring to), adjust the @linkColor:
@linkColor: @orange;