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If you have a logo you wish to use for your store, and you wish to match colors that appear in your logo, you should select a generic template in the Design Wizard. Then, select the color palette that most closely matches the colors of your logo.
After completing the Design Wizard, click the Store Manager link (if you are not open for business) and then click the Store Editor link. Next you can access the Variables page by clicking the Variables button in the Editor toolbar. Here you will find all of the Variables for page elements such as text color, link color, background color, etc. You can then modify the color values of any variable to match or compliment colors in your logo.
If you do not have the color values of your logo, but you do have the logo file, you can get the values in a few different ways: