Sorry I just went through it and it does not tell you how to re engage the motors. Found this on one of the sites.
First, manually open the top as described above (the motors must first be disengaged - so if the red hadle hasn't been pulled, now is the time to do so). Place the top back into its storage bin, and then close the lid of the bin as far as it will go.
Open the trunk so you can get access to the motors. You may need to push down on the storage bin lid so that it closes far enough to allow you to open the trunk - there's a safety interlock that prevents the trunk from being opened if the lid is open at the same time.
Working inside the trunk, remove the carpet liner from the left side (driver's side) of the trunk. There are two plastic clips that hold the liner in place -- you can pry them out with a screwdriver.
Behind the liner are the two motors that work the top mechanism -- one drives the top and the other is for the lid. Each motor is mounted on a spring-loaded pivot mechanism. The gears on the motors normally engage the gears for their respective transmission mechanisms, but when the release lever is pulled the motors pop away and disengage. So you have to push the motors back into their original positions so that the gears re-engage. When you do this the spring-loaded catch mechanism will firmly latch in place. Be sure that the motors arefirmly seated into the drive, and not just partially engaged.
Once both motors are re-engaged, get into the car, and with the ignition key in the off position press and hold the top control switch in the up (for closing) position. Continuing to hold this switch, turn the key to the "accessory" position (without starting the car) and hold it there. After about twelve seconds the lid will be sucked down into the locked position, and then after a few more seconds the top will start its normal closing procedure.
The motors are now re-synched, and should be all set. Work the system a few times to ensure that both motors are properly engaged and all is well.