Here are the steps that I use on a really old or dull knife. This is what Spyderco's sharpening wizards say to do and it works for me.
1. Put some black magic marker on the bottom of both edges.
2. Using the 40 degree setting with the edge of the brown rods make 10 passes on each side.
3. Examine the edge under good light and with magnification if necessary.
4. If I have removed the black mark at the very bottom of the edge then I use the normal Spyderco recommended process which is still at the 40 degree position.
-use brown rod edge until very sharp.
-use the brown rod flats until very sharp.
stop if you want a "utility" very sharp edge (utility I think means there are some microscropic sharks teeth at the edge). If you want a polished edge.
-use the white rod edge until very sharp.
-use the white rod flats until very sharp.
Two things you should have noticed by now. First, don't go to the next step until the knife is "very" sharp with the current step. Second, don't count strokes. Make enough passes as necessary to get the knife "very" sharp.
or
5. If the black mark is still at the very bottom of the edge and but the mark is removed higher up on the edge.
-switch to the 30 degree rod setting.
-use the brown rod edge until very sharp (this could take quite a bit of time but is worth it).
-use the brown edge flats until very sharp.
-go to step #4 and do those steps.
What is "very sharp"? It is a sharpness across the entire edge that will shave hair or cut paper effortlessly.
Now if you really want a shine on the apple, you must learn how to use a strop/hone with some Chromium Oxide paste (CrO) on it.
http://www.drsharpening.com/leatherhone.html
If you really enjoy this sharpening business go to the Toolshed forum. There are some awesome sharpeners there that will tell you more than you could ever imagine about putting a razor edge on a knife. Here is what the Bladeforum ninja, wizard, jedi warrior Joe Talmadge has to say about knives and sharpening.
http://www.bladeforums.com/forums/showthread.php?t=368828
I'll shut up, I'm sure I have exceeded my alloted daily quota of bytes.