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So yeah, how do allies work in a game with multiple force charts?

Is it business as usual? Or a seperate allied detachment for each primary one? Something else?

This is covered in the Allies rules on pages 109-110 of the rulebook, so I'll direct you to them to save me typing them rote.
The important things to note are that you don't have to double up the allies if you double the Prime, and that if you do double the Allies the second has to be from the same Codex (just like the doubling the Prime).

Not to be rude, but Dakka is not a replacement for the rulebook, if you have a specific question ask away, but something so vague is just asking for trouble (for both you and for Dakka itself).