Sorry to read about the top operation concern. The top can be closed manually. What you need to do is open the trunk. There is a access hole located on the left rear of the trunk. This hole should be covered by a round plastic piece about 4 inches in diameter. Remove the cover. Behind this you should be able to see the hydraulic pump assembly. This pump supplies pressurized fluid to two hydraulic rams to operate the top. On the pump there is a small toggle bolt (looks like a T). Turn this toggle bolt to release pressure from the hydraulic system. It should now be possible to close the top.
If the top is locked into the down position by the locking latches, attempt to open the top to get these locks to release.
The most likely source of the top not closing properly is a microswitch. There are 4 to 6 microswitches installed at various positions in the convertible top and latching assemblies. You will need to take the vehicle to either the dealer or a very good independant shop that has the scan tools and know how necessary to check the binary inputs from the switches and know how to "read" these inputs. Your vehicle may very well be covered by the 4 year/50000mile new vehicle warranty (depends on the sale date).
The panel is flashing to let you know that the top is not fully opened or closed.
I hope that this information helps you get the top fixed and operating properly. Max
The black metal box should be the amplifier for the Monsoon radio. There should be an access cover in the left luggage compartment trim. Lean in and look down and towards the rear of the vehicle. There should also be a ventilation grid along the lower edge of the left trim. Both of these components can be removed. I was accessed the VW repair info for your vehicle and the component schematic for the left luggage compartment trim shows both of these covers. I will look again to make sure that this is correct. Max