I have heard in the past labeling CDs or DVDs using permanent markers is not good, as the strong ink of the marker will cause the CD to corrode. So what I would do is to label the envelope or the case of the CD. The problem is when the CD is not immediately returned to the case, so I get mixed up and have to check each one.
Then I discovered these CD markers from Beipa. These are designed to write effectively on the label surface of CDs or DVDs and not cause the sensitive surface to corrode. And I like this brand because it is soooo cheap. And of course it lasts long because I don't write on CDs often. And the best thing is, even if I don't use it often, after a year now, the ink hasn't dried up yet, maybe because I would really remember to put the cap back on.
If, after using it for quite some time and it won't write immediately, just shake the pen downwards or use it to write on another surface just to get the ink going.