Hi bigbroso
Changing theme settings via ThemeMagic tool will be the same as changing LESS file, you can see the declaration for brand colors in this file:
templates/ja_company/less/variables.less
// Brand colors
// -------------------------
@brand-primary: #234269;
@brand-secondary: #f87831; // T3 Note: Add secondary color
@brand-success: #5cb85c;
@brand-warning: #f0ad4e;
@brand-danger: #d9534f;
@brand-info: #5bc0de;
You can check out this doc for more info: http://www.t3-framework.org/documentation/bs3-customization#theme-customization
Remember to backup your site first before changing.
Regards