Sorry I guess I should have investigated this a little more. I finally found the answer at Geniedoor.com Hopefully this info will help someone with the same problem. And it worked the first time!

Homelink in-car programming instructions:

To program a built-in-car transmitter to a rolling code garage door opener (Genie rolling code is called Intellicode, Liftmaster/Sears is called Security plus), you should take the following steps.

Clear out anything previously programmed into the in-car system from the factory by holding down on the 2-outside buttons simultaneously, until the in-car red light starts flashing rapidly. This may take up to a minute. (In a few cases, some make cars require the keys to be in the ignition, or the car motor must be running, or the car door must be shut)
Decide which button you want to make to be your in-car garage door transmitter. Hold your transmitter up near the selected button, pressing both the garage door remote and the selected in-car transmitter button simultaneously. Hold down on the buttons until the in-car, red light flashes rapidly. this sets the in-car transmitter to be your garage door openers make transmitter, but you are not done. You now need to make this in-car transmitter your personal transmitter.
Go to the Learn Button on your garage door opener. The button is usually right next to the area the floppy antenna is connected to the motor head. With Genie it is most often behind the light lens, and flashes red when pressed. With Sears or Liftmaster (Chamberlain) it is near, or part of, the terminal screw board. Press this learn button momentarily. A red light should start to flash or an amber light come on and stay lit. Go back to the in-car transmitter button you programmed and press this button 3 or 4 times, or until the door starts moving. This should set your in-car transmitter to your garage door opener.

Here is a link that might be useful: http://www.geniedoor.com/content/troubleshooting-guides.htm

Did you ever fix the problem with your Craftsman remote? I have the same issue and noticed that, after erasing all codes, I can program either my remote or keyless entry, but not both. (The one I program first works, the other does not).