Aha! Time for the Flag Police!
USPower Squadron says from the end of the gaff, if you've got one, otherwise from a pole at the stern, which if it can't be in the middle should preferably be on the starboard side. (Maybe the French prefer the port side?)
The State of Maryland actually has a law that says, for a ketch rig, either at the stern staff (doesn't say middle, port or starboard - whew!) or 2/3's up the leach of the mizzen (or at the gaff, if so rigged). They also require the flag to be a Yacht Ensign (13 stars and an anchor, not a US country flag). Odd law that you can't fly an American Flag on your boat.
Other "authorities" say you can fly it from the backstay, rather than the leach of the mizzen, and Captain Henri said you can fly it from the topping lift.
I"m sure there are 67 other versions of this, so no need to get our knickers in a bunch (well, unless you're in Maryland - jeees, an actual law.)
Cheers, Craig SN68 Sangaris