Sharpee is fine wont hurt anything. I have used a pocket knife to mark my disks before while copying in the field. I marked one with a bit of pizza sauce which I dont recommend. Soon though you will discover the joys of labeling with label stickers. Now any disks I burn I rip the front covers also and print them. The copy looks just like the original until you turn them over and see blue vs silver then you know which is the copy. Use this site: www.cdcovers.cc/ for all the disks youve done and need covers for its easier then ripping all your disks again in your scanner. You can also buy the labels on ebay in bulk or get them at this site:
www.supermediastore.com/