To add additional files to you script you can do this in two ways:
Before Version 5.4
1) Place them in a template file (.tpl) and run InnoSript using template processing.
2) Create a dependency file for your application with the additional files in it and InnoScript will use it and add them to the script.
Version 5.4 and after
Use the Add Files Button to add the files you want to be included in the script.
Use the Add Folders button to add all the files in a selected folder.