I'm a garage door mechanic and the rolling codes gave me some problems as well. Its not very clear in the instructions, but you have to follow BOTH sets of instructions (for non-rolling AND rolling codes).
I'll give you a step by step just to give you an idea, you can fill in the rest from the instructions.
1) Clear the codes in the truck
2) Program the truck using the non-rolling instructions (Holding the remotes very close to the buttons in the truck)
3) After you get the truck programmed for the non-rolling, go ahead and program it for the rolling code now (Using the smart button on the operator and holding the button in the truck)
That should do it, but like I said just take the steps I gave you and compare them with your truck manual and it should be fairly easy to figure out. If you still have problems let me know.