I have made mirrored components outlines to be placed on the top but mounted on the bottom. I did this for the first few bottom mount connectors until I learned how to move/place the parts directly on the bottom layer. For this board due to the SMT parts, the parts must be placed on the bottom. As jpanhalt mentioned, as I change the layer the component is on, the pad colors change. But for some reason I am getting clearance violation between the parts on the top and the bottom.