My experience with customizing a WA template is in a word, painful, oh, and time consuming. You will need to go to Settings/Site look and feel. Check out Styles and Color for the basic settings.
But, there are lots of elements that need to be edited-many you can find in the CSS customization option. Tip-make a copy of the original before you modify it-and add your own comments to keep track of what you're doing. It's best if you have all the html hex colors identified. I use a great ap called ArtDirectorsToolKit which has a color identifier feature to figure out what hex colors are in the template. You can search the CSS code for hex values and replace with your own.
But, and this is where it get's realllly time consuming, there will be still other elements you will have to find by using a browser html inspector-like Firebug for Firefox. WA is best if you don't have a lot of customization to do to the templates. Find a template with as close to the color scheme as you can get.
Good luck. Customizing WA templates is not for sissies.
Jan