Use ftp to copy a theme folder and give it a new name. Files are in root/templates/ja_university/themes…
You can then go to Template Manager/ja_university/ and click themes tab and see if your new one is there.
Using the Profiles tab I would create a new profile ‘my colour’ and then you can assign your theme to this profile using the themes section in advanced settings further down the page. So now you have the site set to your profile and your theme.
Now comes the hard part as you have to go through all the css files and change the colours within your theme i.e. root/templates/ja_university/themes/my_theme/css . Load any new images into the image file to suit the new theme.
Shouldn’t take you too long to do. 🙂
Have fun!