The AppDynamics start up appagent command must be put in the startup script of the application. In the case of ALM this is in the wrapper.conf file.
Go to the ALM Server and follow this path to the correct wrapper.conf file:
By default the Program Data directory is hidden. If you don't see it in your C: directory you will need to show hidden folders and files in Windows.
Click on ''Organize''->Folder and Search Options->View->click the radio button of the ''Show hidden folders, files, and drives'' to see the folder.