Sure, for the header menu, you can edit your chosen theme in skin/reboot/css/themes/xx.css, eg.
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.menu-container { background: #0d47a1 !important; }
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And/or, in skin/reboot/custom/reboot_css.tpl after...
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{load_defer file="css/bootstrap/bootstrap.min.css" type="css"}
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Insert...
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{load_defer file="css/bootstrap/bootstrap-theme.css" type="css"}
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Then edit skin/reboot/css/bootstrap/bootstrap-theme.css
I've added this as a template option in the latest version.