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So we have Android device (with USB host support) and Arduino Uno board connected using USB OTG cable (blink sketch is uploaded)
launch ArduinoCommander app
tap "Menu" / "Upload sketch *" menu item
choose "StandardFirmata (Uno @ 57600) sketch" menu item
tap "Discover devices" and tap on USB device in the list
allow USB device access
tap "Upload" button and see uploading progress
now return back and connect to Arduino board
turn pin 13 on to check connection
LED on pin 13 is on
now upload bundled blink sketch back to the board
now LED on pin 13 is blinking