If it is an 1100 yd spool, I use a zip lock sandwich bag and peel the tag off and place it on the inside of the bag. When I take the spool off my sewing machine, I put it in the bag and zip it, then replace it in the embroidery thread box. If I'm using the 5000 or larger spool, I write it on the inside of the spool. If I have more than one of the same color, then I just refile the used spool next to the new one without doing anything else.
Edited to add: I bought several thread kits of 100 spools off Ebay when I first started embroidering. Two are polyester and one is rayon. I make sure I keep the spools in their kits. I don't like mixing threads when embroidering.