I typically use Armorall wipes for general cleaning of systainers and tools. I believe that was a tip I picked up from one of Sedge's videos.
Though I've not had sharpie on a systainer or other textured surface, I know dry erase marker typically removes it from other surfaces. Scribble the dry erase over the sharpie mark; the old ink rehydrates and both wipe right off. I'm not sure if it'd wipe off as easily with a textured surface, but for smooth surfaces (white board, leather, etc.) it's worked in the past.