I forgot the batch files. But now here is my solution.
The batch SignApp.bat is on an central place. You must change the paths, the keystore names and the alias names. At the moment, it is designed for two different keys.
The Batch Sign.bat is for the app source directory (one copy for each app). In this file you must change the location of SignApp.bat and the app name. For signing you only start the batch file with or without the keystore password as parameter.