If the CPs aren't sticking to the bones you missed something.
You dont' mention that you tested it in an "action" (putting it in a choreography will work too). FlowerPower mentions this at the bottom of the page "Assigning control point to bones" and just before it discusses Smartskin.
The CPs won't stick to the bones in the modeling window, because if they did it would be impossible to change the position of a bone in relation to the mesh without haveing to reassign them to some other bone first.
Guys, I believe I have the Bones issue ironed out and the fish animating (swimming). When viewed in different angles I can see where I could improve but it would require a lot more work then what the project asks for. Not wanting it to look crappy, i'll redo the whole thing and make it look nice.
Thanks for everyone's help, links and patience. I'm going to go over all of the demos you've all posted and post my FINAL version when I get better at animating, modeling, etc.
SMC
Fish_Swim.mov