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So lets say that my Wyches, headed up by a Succubus with an Agonizer, are locked in combat with 2 units, one of which has a 3+, the other of which has a 2+. Call it Greenwing and Deathwing. The Succubus is in sole base contact with one of the DW. She rolls a 6 to hit. The Agonizer AP3 is worthless against the opponent she's in base contact with, but will work against a GW. The verbiage of Precision Strike says 'Wounds from Precision Strikes are allocated against an engaged model of your choice in the unit he is attacking...' However, technically the unit that I want to allocate the wound against is different from the unit I am in base with. Can I allocate the wound anywhere in the combat that I please, or am I stuck allocating it amongst the unit I'm in base with?

The only stipulation to precision strike is to an engaged model so i don't see why you couldn't allocate to green wing.

Edit: woh woh woh I think im wrong.
"Wounds from Precision Strikes areallocated against an engaged model (or models) of your choice "in the unit he is attacking", rather than following the normal rules for Wound allocation."

As it must be allocated within the unit it is attacking i am unsure how that works with primary and secondary targets in multi combat.

Right. Exactly. That's the source of my question.

"In the unit you are attacking". This is perfectly clear. If you are in a multiassault, a given model's attacks are made against the unit they are in base contact with, and cannot wound any other unit. If a given model is in base contact with models from multiple different units, you must declare exactly which unit(s) that model is attacking, before rolling.

Precision Shots specifically say that you still have to allocate those hits against the same unit you attacked.