koz

If you transfer ipa files to your iPhone under this directory: /var/mobile/Library/Documents/Intallous/Downloads
you can just open Installous and select Downloads (on the bottom of the screen), you will see the ipa file/app that you've just transferred on the list, just tap on the file, the app will be installed into your iPhone automatically.

You don't use iFile to do the file transfer.  You should use WinSCP or iFunbox.