You press the stamp just enough so you can see the design. It doesn't really matter if it does make a deeper mark as I thin my paints with melted cocoa butter and they do not have that pooling effect. If it does go down in the groove it only goes down on the side of the design and not up the outer edge. I don't know if that makes any sense, but it does work.
Another method is to use stiff stencils and press the stencil into the fondant. This raises the design and it's easy to paint that way also.
When you use the melted cocoa butter you get a shiny finish to your work.
Hope this helps.