_variables-project.scss holds my project specific vars such as colors and stuff that is not directly related to Bootstrap.
_variables-bootstrap.scss holds the Bootstrap vars that I want to override.
You could of course skip the bootstrap specific file and just put everyting in variables-project (or whatever you want to call that file).
@import "variables-project";
@import "variables-bootstrap";
// Automatically injected Bower dependencies via wiredep (never manually edit this block)
// bower:scss
[rest of scss-code]
According to documentation for bootstrap, we suppose to copy variables and other custom stuff into the bootstraps _custom.scss. But you are right, bower folder shouldn’t be touched
if you really need you should be able to override and decide about every file what will be injected to your main.scss from bootstrap
@import "common/variables"; // write your custom variables here that bower injected files can read them
// Automatically injected Bower dependencies via wiredep (never manually edit this block)
// bower:scss
@import "../../bower_components/bootstrap-sass/assets/stylesheets/bootstrap/_variables.scss";
@import "../../bower_components/bootstrap-sass/assets/stylesheets/bootstrap/_mixins.scss";
// endbower
// and add other files from bower.json to override
@import "common/global";
@import "common/type-custom";
@import "components/text-ribbon";
...