To access skinning editor press Ctrl+Shift+S, either during gameplay or in the song selection.
For the key counter you have either
ArgonKeyCounterDisplay
or
DefaultKeyCounterDisplay
. Just click any of them, it should appear at the center of the screen, and move/resize it as you wish.
For the box in the difficulty pop-up, I think you were talking about the song select screen, you can't change the appearance of anything.
And to import images, you can import a sprite that was on the skin folder using the
SkinnableSprite
element, then at the right of the screen you choose which image to show. It works both in song select and during gameplay
Hope it helps