ok, so step one, have the paint.net shortcut in a place where things can be dragged to it. Next step is to navigate to
C:/Program Files (x86)/Steam/steamapps/common/vvvvvv/data.zip/. After that, copy the graphics folder into the vvvvvv folder in your documents. Open the copied folder and find sprites.png. Drag that picture into the paint.net shortcut from earlier to edit it. I recommend creating a temporary layer to outline the borders of each sprite as to not have anything get cut off. Simply save it once you're done and launch VVVVVV. Putting the graphics folder in the vvvvvv folder in documents tells the game to use those files, so your sprites will appear!

PS: NEVER alter the VVVVVV folder that's in the steam folders, because ANY changes to it, such as adding a file will cause the game to never launch again, and you'll have to re-download it!