Hi.

I have heard some military comms on my scanner (not that I understand
everything I hear).

If I understand correctly, "Flight Level" or FL is used to describe
altitude. So, FL400 would be 40,000 feet?

Nope.

http://en.wikipedia.org/wiki/Flight_level


My question is, if an airplane is way up there, can I hear the plane down
here? (I can hear them on the radio, but I mean, can I actually hear the
engine of the jet, as in the sound that a jetliner makes when it goes
overhead.)

What you hear is the sound of the engines. It is louder than the "sound that a
jetliner makes"

At the speeds used up that high, wouldn't I hear a sonic boom?


Not when the plane isn't going supersonic.

Wait til high school. Your physics teacher will explain.