You can do this for any app from PortableApps.com for example if you want to pass command line argument to GoogleChromePortable, go to [X]:\PortableApps\GoogleChromePortable to folder Other\Source and copy the file GoogleChromePortable.ini to your
Where [X] represents your drive letter where PortableApps directory is found.
Open the file in text editor and find:
and change it to any value you want to pass to main app, for example proxy definition:
Save the file and run the portable application again.