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The Store has a number of schemes that you can select within the Store itself. The scheme then is applied to the whole of your Store. You may also customise this as a color scheme of your own creation.
Ecwid have a very good FAQ on this process and some specific questions related to how and limitations
I think the problem is that the colour scheme I have chosen is dark and I have put in widget panels in a lighter colour, then widgets within those. I may just need to drop the lighter panels, but will have a look at the FAQs first to see if I can work around it.