Can you use EAC to take pops/clicks out?

I assume that you are recording the CD to WAV and then using the WAV to burn a rw-cd. There’s an extra step in the middle to edit the clicks out of the WAV file. More complex pops that occur on analog recording (tapes, etc.) should be found by listening to the WAV roughly to find the positions with +/- 3 seconds accuracy. Then select such a range and choose “Pop Detection”. Usually EAC will find them automatically. If not, switch to “Spectral View” and look for any anormalities. Then you have different options to remove the pop.