When you want to change the Query Builder’s appearance you need to override its style sheet. While you could modify its own style sheet, that is not the recommended way. To make it easier to upgrade the Query Builder in the future, your modifications should be stored in a separate CSS file. For example, if you store them in a file called yourCustomJCSDLCssFile.css, you will have to inlude yourCustomJCSDLCssFile.css after you include jcsdl.min.css.
<link rel="stylesheet" type="text/css" href="jcsdl/jcsdl.min.css" /> <link rel="stylesheet" type="text/css" href="yourCustomJCSDLCssFile.css" />
For a more in-depth overview of the Query Builder theming options, take a look at the CSS resources page.