I assume that it is the flipper door that is rubbing on the tonneau cover. If this is the case then yes you can adjust it by opening the flipper door to the straight up position then turning off the key. With the door open you eill find four nuts on studs under the main door. With a 13mm wrench you can loosen these, one side at a time, and adjust the flipper door forward.
The keys are not what sets the seat positions, but the remote key FOB does. TYo set the seat positions,there is are two number buttons on the side of the drivers seat. Once you have the seat in position for driver one press and hold the number one button for about three seconds. Repeat this proceedure for driver number two, but use button number two this time. At this time when ever you use the remote lock (#1 or #2) to unlock the vehicle, it will automatically set the seat positions for whom ever is driving.
The front satin bar is attached with two 7mm bolts near the inside corner under the hood, and with pressure clips along the bar towards the headlights where it is velcroed on the lights. Might be worth removeing it to see just what the problem is.
For the service manual, you may want to try www.gmpartsdirect.com
Hope this helps.