for sps i usually remove them and just epoxy tem but most of the time i leave them attached and drill the rock or cut the stem off and epoxy them. i do this because if i get a rock covered in coral such as xenia (my issue right now) and i remove that rock from my tank to sell it and get a replacement that is not the same size then i have to re-aquascape the tank so i end up moving some of the plugs around to make it look good.