Unless otherwise noted, assume an empire as CEFO-I, II, and III plus IA tech.
Pre-X tech example: CVA(CWE,2xDWE), assorted other ships, CWE=20AF, DWE=15AF. Any of the escorts in CEFO slots would do follow the (D19.10) damage procedure. If all three were in CEFO slots, the damage would be 50% of 50 (20+15+15).
X1 SQ: 4xCAX, 6xFFX. Via D19.40, the damage for being X ships is 4*1 + 6*0.5 (7 points). Since the SQ is entirely X ships, this is doubled to 14. Ships being in reserve or Fleet Formation slots doesn't change the damage.
X2 SQ: 3xXCA, 3xXDD, 3xXFF. Via D80.200, the damage from D19.40 is double what it'd be were the ships X1 ships. This means each XCA does 4 (1 via D19.10, doubled for being X tech, and doubled again for being X2 tech) and the SC4 X2 hulls do 2 points each. Ships being in reserve or Fleet Formation slots doesn't change the damage.
X1 CV group in an X1 SQ: If an empire had an X tech CV with X tech escorts (most empires have X tech CSVs, but few have X tech escorts), the escorts would use the D19.10 procedure (if they were in CEFO slots; no extra damage for being X1 ships) and any other ships would use the (D19.40) rate (make sure to double it since the SQ is entirely X1 ships). Ships being in reserve or Fleet Formation slots doesn't change the damage.
X2 CV group (conjectural ship designs). If the escorts were X2 (and the CV required them), the normal D19.10 procedure would be used. Ships being in reserve or Fleet Formation slots doesn't change the damage.
If the empire does not have CEFO-I, II, and III, then the X1 (or X2) special damage rules don't apply (empires with CEFO-I or I and II would do some damage via their escorts, but not the bonus X tech ships damage).
This is messy; examples when you lack CEFO-III tech have been skipped, as the X tech bonuses require it.
SQ with a mix of X1 and X2 ships, no ships using CEFO slots - X1 ships use the D19.40 rate, X2 ships use the D80.200 rate. Ships being in reserve or Fleet Formation slots doesn't change the damage.
SQ with a mix of X1 and X2 ships, X tech CVs (X1, X2 or both)- use the 50% AF rate for escorts using CEFO slots and the D19.40/D80.200 rates for the remaining ships.
SQ with X2 and non-X ships: The X2 damage drops to 1 to 3 per ship (unless the ship is in fleet formation or reserve, then it is 0), via D19.30 and D80.200 (X2 CV escorts not in reserve would get their 50% AF, 0 if in reserve).
SQ with X1 and non-X ships: The X1 damage is 0.5 to 1.5 per ship (unless the ship is in fleet formation or reserve, then it is 0), via D19.30 (X1 CV escorts not in reserve would get their 50% AF, 0 if in reserve).
If for some insane reason you have X2, X1, and non-X ships in the same SQ, the damage follows from the previous two examples.