I'm sure a lot of fly fisherman out there have multiple spools with different lines on them for each reel. If you don't then I hate to break it to you but you're either paying way to much money for way to many reels or you're not making use of some awesome lines out there. There are so many lines on the market that if you're like me and you've got a lot of them it can be difficult to keep track which line is on what reel/spool.
I like to mark my spools to keep track of all my different sink tip lines, shooting lines, floating lines, cloths lines, etc. To do this I put a little dab of nail-polish somewhere on the spool so that I can distinguish one line from another. This works great because there are a million colors of nail-polish and it is waterproof/durable. Just remember to make a key on a piece of paper somewhere otherwise marking them is pointless.