This is also what I do.

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.

how to keep # on thread
 

I use a magic maker and write the # around the bottom of the spool

Thanks for all the great ideas. I will put the carefully removed labels inside the bottom opening as this seems like the quickest, easiest way. I like the idea of a campaign to the manufacturers to ID these thread colors in more than one way!!

I too write the no. on the bottom of spool with sharpie, My problem is knowing rayon from Poly. forgot to mark that and now it is to late. already mixed up. any ideas for that?

Rayon will change color or fade with bleach, poly won't...so maybe you could mix a small batch of bleach and water and dip the ends of thread in...wait and see!

You might be lucky ....... Some of the brands change the colour of the spool according to the thread type and/or weight.

Thanks everyone for the great ideas. I "store" my spools in the original box, helter-skelter with thread winding around everything. The idea of putting each spool in a little baggie with the number written on the outside is so great! Then the bags can be "stored" like the spools, but the threads are contained and the colors are numbered. Thanks again to all.

Thanks Donna, I will try that. I did not know about that.