Save your input using the Save or Save As ... menu commands.
Your input will be saved in a file with the name you specify, and at the same time a run script will be saved. It has the same name, but with '.run' appended.
This script contains most commands to run your calculation. However, typically some more administrative things need to be done: make emty working directories, make some links to follow a running calculation, etc. This used to be done by the run script, but not any more. If you wish to use the run script yourself you are responsible of taking care of such details.
To run your calculation, use the Run command from the File menu. This will tell ADFjobs to run your job. Alternatively, you can switch to ADFjobs, select your job (that you should have saved from ADFinput), and select Run from ADFJobs Job menu.
In ADFinput, the panel 'Files (Restart)' you can specify what files to save at the end of the run script.
By default, TAPE21 (result data), TAPE41 (grid data for visualization) and TAPE13 (checkpoint information) are saved.
If the environment variable SCM_RESULTDIR has been set, the run script will change into that directory. Next it will run from there, and all result files will be stored in that directory.
If the environment variable SCM_RESULTDIR has not been set, the run script will execute in the directory where it is started, and the result files will also be located in that place.