I am using the medium rods and when they didnt work i tried the fine rods to see if it would remove any burr that might be there. I am not certain what a wire edge is or how to check for it.
I tried a different knife with the sharpie trick, and realized that that knife would also have to be totally rebeveled because the edge angle was way different that the 40deg on the sharpmaker.
Two big problems here. First you need to understand what a wire edge is and second you misunderstand rebeveling.
There is no need to rebevel to put a secondary bevel on a blade. You only rebevel to make the edge sharper (thinner) or stronger (thicker) for regular use. You definitely do not want to rebevel to match a sharpening system's settings.
If you have a thin grind and you put a thicker/more obtuse secondary bevel on it, that secondary bevel is there to protect the thin grond from deforming under stress. By reprofiling the whole grind the same as the secondary bevel, you are creating a Scandinavian grind. You don't need this.
Now for the wire edge. When you sharpen, you want to make both sides of the blades meet evenly at the same angle. At the extreme edge, this means you are down to molecular levels of thinness. This is a very weak amount of metal, and will bend from side to side as you use the knife.
This is the wire edge, or burr. You need to break it off to leave a very thin, but more robust, edge. To do this on a Sharpmaker, run the blade down the rods but at a higher angle than you used to sharpen it, that is, pull the back of the blade slightly farther from the rod on the downstroke.
Even more helpful, strop the blade. I do this all along on a pants leg or a leather belt. (Stropping is pulling the blade over the surface, back first, rather than sharpening, which is edge first.) If I have an obdurate burr, I will even strop right up the Spyderco rods themselves first.