Don,
Yes, both of my antennas, send and receiver are in a horizontal position. Works very well in my plane like this.
Good question. It will actually mess with things if you alternate using the iPad with the SkyGuardTWX App and the iFly GPS software to change the squawk code. The SkyGuard App claims comm port priority and then blocks out the iFly GPS communications. Both work fine if you use one or the other, but not both at the same time. If you are going to use the iFly GPS app to set the squawk, just make sure the SkyGuardTWX app is completely closes and not running in the background.
You can change the Squawk from inside the iFly GPS app. Touch Menu and you will see a SkyGuardTWX Control Panel. Additional, you can add the ADS-B Status instrument and you can simple tap it when the squawk code is showing and it will shortcut you to the control panel to change the squawk. Hope this helps.