I put my initials on my skis via a Sharpie then put a symbol onto them. There are some valid arguments as to why and why not label them. My personal habit sets up so that I swap them each ski day. The most valid reason I have seen thus far is that if you have a problem with one, you have at least narrowed the issue to a particular ski if the issue is not inherently obvious.
You should exchange one of your skis with someone else who has the same skis and ski on two Left skis (or two right skis.) This is the best way to deal with the issue, then you don't need to mark them.