Question about 2006 Jeep Grand Cherokee

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After going through a large puddle it now has a knocking noise coming from the rear of the engine, all cylinders have spark

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From what you've said, it sounds a lot like you have broken a connecting rod (the part that connects each piston to the crankshaft). When you go through deep water or a large volume of water is splashed up, there is always a chance that it can enter the intake.
Water is not compressible. Since the engine is turning and not all cylinders fill with equal amounts of water, the engine is still trying to run. The "weak link" is either the connecting rod or the top of the piston, so either the rod bends, breaks, or the top of the piston caves in.
'Though you see Jeeps and other 4x4's thundering through rivers etc in commercials, to safely do that, an engine needs to be specially prepared, sealing the electronics and raising the air intake higher up.
Extreme versions of this extend the air intake with a large diameter pipe that stands even higher than the cab. Jeep intakes are reasonably high and in most cases won't have problems under normal conditions but if you hit the water just right, it can and does get in there.
Unfortunately, the only way to determine exactly how much damage was done, your engine needs to be torn down (at least heads and oil pan need to come off) If there isn't any block or crankshaft damage you can replace the damaged parts. Otherwise, the engine needs to be replaced.

Posted on Apr 06, 2011

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The knock sensor (KS) system enables the engine control module (ECM) to control the ignition timing for the best possible performance while protecting the engine from potentially damaging levels of detonation. The ECM uses the KS system to test for abnormal engine noise that may indicate detonation, also known as spark knock.

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