You can install more than one exe in the app path, is there a reason why you are trying to install them in seperate sub folders and not in the installation path?
If the files have different filenames then there is no reason I can see as to why they could not be in the same folder(s). As for can it be done I am sure it can just never tried it. The source code for the setup generator is included so it is possibel to modify it in many different ways.
For example I have modified mine to read additional values from an ini file and in some cases the installer will prompt the user asking if they want to place a shortcut on the desktop and/or it they want it added to the startup menu.
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