The extra FLAT antenna is a 5.8Ghz "PATCH" antenna. It replaces the mushroom antenna.
The Mushroom antenna is more OMNI directional, the flat Patch antenna is quite directional. You need to make sure the flat part faces the aircraft at all times. The patch antenna can give you more range for your video receive, it does NOT affect the radio control of the aircraft.
Use the Forum search (Magnifying glass) at the top of each page. Do a search on ANTENNAS, you will have tons of reading to do.