In my fpd I've got a layer which is over everything but everytime I'm uploading a picture and I want to resize it, it's not working because the layer being over everything is chosen. This layer is important because my customers should be able to pick colors. Is there a way that the customers can only change the colors from color picker for the svg with going to the "Mange layers" tab?

Overlay layers can only act as masks (click through) when they are not modifiable in any way - that's why this won't work.

I'd recommend that you create one fancy product per color and then use the change product feature, similar to this demo: http://fancyproductdesigner.com/product/hats/