Thanks, I got all the art swapped out now for the in class ball point pen doodle kinda style I'm going for. I need to pick up some graph paper so I can do better hand drawn tile maps. My process right now is basically draw on printer paper, scan it in, get rid of the white background, and line everything up in Photoshop. What I like about it, is I can add any enemy I want just as a persons doodle. I may even have some friends try and draw up some stuff.
If you are still seeing dark black pixel line art you may need to clear your image cache for the art to update properly.