A 2x2 or larger enemy is laid out exactly the same as a 1x1 enemy, you just use the tiles for the top-left corner of the enemy and set A.SkipX on its combos to one less than its tile width.
As far as I can tell I have it laid out correctly (but obviously I don't or else it would be working). I have 4 2x2 boxes (so 16 tiles total) in a row for up, then the same amount under it for down, again for left, and last for right. I then have the same amount of tiles next to those for the firing animation. The combos are first the top left corner of the up animation, then to the right of that the top left of the down animation, then left and right, then under those four combos and the same thing but for the firing animation. Each combo has 4 animation frames with a speed of 5 and A.skipX is set to 1. Within the enemy editor I have Misc Attribute 11 set to the first combo which is "up". In game when it moves it only shows the up animation when moving, then shows the walking down animation for a moment when firing.