The ISSetupFile table (which controls the support file template) only supports extracting files to a single directory. There is no way in the user interface to say that it is dynamic, although you can have a build automation step that reflects the contents of the directory and connects it to the table using the automation interface. However, this still could not do subdirectories.
What you probably want to do is create a self-extracting ZIP file of the files you need as part of your assembly and add EXE to support the files. Then write the special actions that the EXE calls to extract the payload to support files and another CA to clear it. Take a look at the user actions of ISSetupFilesExtract and ISSetupFilesCleanup to find the best way to do this.