Does it matter whether the antenna is attached to the male or female connector side of the filter?
Are you talking about the Flightaware filter? I have one and have tested it both ways round. I didn’t see any difference.
I’ve read it don’t matter but I hooked mine up the way FlightAware answered the question on Amazon.
Which connector is input and which is output?
The SMA male connector (to the right of the image nearest the end of the "Flightaware logo) connects to the receiver. The SMA female connects to the coax cable from the antenna.
By FlightAware on October 2, 2015