How do you manually close the fully auto top on a 1996 328i bmw?

Most have a seperate crank to open and close top in case of an emergency ....If you have checked all fuses,relays,..etc..and know motor is broken you can remove the drive from the motor and raise it manually by hand with an assistant on the other side..

try a spray lubricant into the motor mechanism and grease any visable wire cables that run from/to motor ,not the electrical cables the bare wire winder cables,also grease/ lubricate any accessable pivot/hinge points , gently pull the cord and gently push the roof back and forth occasionally trying motor with a bit of patience this should get the roof moving , also look for anything that may be snagging the roof/mechanism as there is a pressure protection system to stop the roof being fully closed on say someones hand so preventing injury

indicating a micro switch failure or that the top clamps are not fully closed. make sure the rear handle under the seat is fully retracted

There are 2 motors that have to be put back in place one for the top & one for the top cover... If you have reconnected both & still have problems you can resynchronize the top by rolling down all windows, hold the top button in the close position before turning the key, turn the key on and wait for the windows to close & the red light to stop flashing.

If this doesn't work pull the release arm, manually lower the top, (to get into trunk the passenger side of the top cover needs weight on it to engage micro-switch to release trunk lock)

reconnect motors, hold the top button in the close position before turning the key, turn the key on and wait for the windows to close & the red light to stop flashing.

Happens alot. If you or someone pulls the interesting red strap under the rear seat, you have to do a reset. You have a small shot at just re-engaging the motors but will probably have to do a full reset. Take the back seat out and push lever back into the correct position. If you have a semi auto top (have to manually unlock top where it meets the windshield), lift the top back until you can pull up the back of the top to access tonnau cover. If it is a fully auto top, you have to pull out the cover at the very front of the headliner to access manual crank port. There should be a small allen wrench in the trunk tool box. You have to crank and crank and crank until the top is slightly open. You can then lift the back of the top to access tonneau cover. Both top types are the same from here on. Lift up on the tonneau cover and stow the top. Have a friend (or a heavy tool box) push down on the front part of the cover on the passenger side. You will hear a click. This will allow you to open the trunk. There are two motors located in the driver side rear quarter panel. You have to take out the covers hiding them. One motor is sort of in a horizontal placement under the pan where the top is stowed. Push up on this to re-engage. Other motor is in a vertivle orientation and at the driver side rear quater panel. You have to sort of grab the motor with both hands and pull it back into engangement with a gripping motion. Close the trunk. Push the switch to close the top (forward) and hold it down. Insert the key and turn it two clicks (accessory). After about 10 - 15 seconds you will hear the tonneau cover close and then open and the top closes. Let it cycle through and you are done. Hope that helps!

No doubt your soft top issue has long been resolved but just in case someone has a similar issue:
I started to open my A4 Soft top externally using the door key method and like an idiot I must have disengaged the key before the soft top was fully down. I was unable to activate the opening or closing of the soft top automatically using either the key or soft top switch inside. I then manually closed the soft top using the users handbook and manual tool supplied. Soft top would still Not open automatically and the soft top alarm would activate. I solved the issue by manually opening the soft top fully and then manually closing the soft top fully. This seemed to have reset whatever had gone askew.

My bonet on my 1 series wont close properly it doesnt appear to be catching in the release lock although the mechanisim is working when I press down on it manually. The bonnet is only staying shut because the opener catch/hook is working, but this is the only thing holding it closed.

The convertible top motor and release lever are in the luggage compartment.
From the Bentley manual, the following general procedure is suggested in order to close the top in an emergency situation.
Main motor. To release the top linkage from the motor, lift the left corner of the rear seat to access emergency release handle.
It is then possible to push the top manually to a near closed position. In case of the semi-automatic top, simply attach and lock the front latches.
Front latches. Once the fully automatic convertible top has been released from the motor and manually pushed to near-closure, emergency latching of the top is possible by using the S-shaped hex key provided in the emergency tool kit(attached to the trunk lid underside).
First, remove the the plastic cover over the latch motor in the front bow of the convertible top.
Next, use the hex key from the tool box to crank the front latches shut.

top still needs to be adjusted to fully seat properly in the trunk/boot. if the upholsterer who replaced the top is not familiar with the adjusting process for a BMW, then i would take it to a BMW dealer and have them do the final adjustments.

i have a 325i bmw convertible and by mistake i pulled the release bar under the back seat and detached the motor for the convertible and know it doesnt want to open or close the convertible