A complex design may make you want to color code some areas. If this is the case, you may want to use dry-erase markers. These are the markers that you use for a white board at work. They write on the pumpkin surface well and clean up easily. Pens and other markers don't come off of a pumpkins skin and will make you were absent on the school day that they covered staying inside the lines.
If you can't bring some dry erase markers home from the office, they are available at an office supply store. If you do bring them home from work, bring them back when you are done. You probably won't use them again until next year and by then they will be almost dried up. You can wipe the tip clean with a rag and they seem to work well again.
One note, dry erase markers don't work on a wet surface, so try to dry off your pumpkin before you draw. Also, the markers won't write if they get pulp on them, so if they stop writing, rub them with a rag to get the tip clean again.