Okay by the numbers....
12 phaser banks =
Saucer TOP: 1 bank port, 1 bank forward, 1 bank starboard = 3 banks (3 so far)
Saucer TOP: Impulse/Engineering 1 bank port, 1 bank starboard = 2 banks (5 so far)
Saucer Bottom: bank port, 1 bank forward, 1 bank starboard = 3 banks (8 so far)
Port Bottom warp pylon: 1 bank = (9 so far)
Starboard Bottom warp pylon: 1 bank = (10 so far)
Hangar bay top: 1 split bank of 2 phasers = (11 and 12?)
Megaphasers: 1 port and 1 starboard on either side of the navigational deflector
Photon torpedo launchers 1 port forward, 1 starboard forward above the navigational deflector
Photon torpedo launchers 2 aft below the hangar
Did I miss anything?
My current tactical view of the Challenger Class conversions that have been done so far is that, if I had to attack it, I'd try to attack it from behind just above the rear facing hangar or directly from below dead center under the engineering hull where there are no phaser banks.
Now, I'm not saying add more weapons. I'm not a huge fan of Federation fanboy "you can't scratch the paint on my ship" uberships. The Challenger class was supposed to be made from off the shelf TMP parts. I'm just suggesting that the conversions done so far haven't 100% accurately reflected what is on the blueprints. None of the three versions of this class I have show the phaser banks on the bottom of the warp pylons...
I'd like to believe that the Challenger class has a variation in overall capabilities like the differences between TOS Defiant or TOS Enterprise. A good non-canon example of this could also be LT. Kevin Riley's USS Phobos, a TMP FASA Loknar Refit. His original version and P81's version varies in the number of phaser banks on it's saucer for instance.