I reprofile with the new diamond rods on the sharpmaker. The magic marker can be quite helpful in regards to reprofiling. The diamond rods are expensive, but easy, $56.00 per pair from New Graham. I can get ATS-34 blades really sharp in a few minutes. I can get VG-10 blades incredibly sharp even faster. I had read previously other posts that it was hard to ever get a serrated spyderco as sharp as it came from the factory, but I honestly think that both my Calypso Jr. and my Veile (VG-10 blades!) are sharper than when they were new. Still haven't tried it on my Boa CPM-440V (hope it's not as bad as Buzzbait says, but he's been right on everything else I've read from him--think it's going to not be a fun one to sharpen).
My recomendation is to clean the stones as they load up with metal, the corners, the most useful part of the stone indeed, load up much faster than the flats. I use small pieces of scotch brite pads, with some soft scrub on them, but any abrasive cleaner would work, as would rags in place of the scotch brite. Your knives are going to be sharp very soon now! Best of luck.