Hi, sorry about your problem. It would seem that you will have to figure out why your trunk won't open first & then you will be able to close the top manually. What kind of alarm are you getting?
If you can finally get your trunk open go here for the procedure to close it manually.
Factory Service Manuals - NICO Club The procedure starts on page RF-24.
You will have to get the top up to troubleshoot the problem. Good luck & let us know how it goes.