1) Once you have processed your filled jars, write directly on the (new) lid in permanent marker. Then you can easily tell the difference between previous used lids and new ones. The lids should only be processed once, but I reuse them for storing dry goods.
2) Write on masking tape with permanent marker and affix to the glass jars. The tape sticks well enough, but is much easier to remove than canning labels and much cheaper!
I usually label both the lid and the jar so you read them no matter how you are storing your jars.