You must have the AIR SDK installed to sign an AIR application.

For convenience make sure the /bin/ directory of the Adobe AIR SDK is in your PATH environment variable.

Open a command prompt and go to the source folder of your AIR application (the source folder is the one that contains the application.xml file).

Run :
adt -package -storetype pkcs12 -keystore <full path of your PFX file> <Full path of your .air file> application.xml .
(be sure you include the trailing period)

For a more complete tutorial, please see