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How should the psychic phase play out in apocalypse? Can all dice from both armies be used to cast/deny?

What do you mean by 'both armies'...?

There are no rules to cover multiplayer psychic phases, like that in apocalypse.

This is what I would do. Every player has their own warp charge and deny pool. Only the player targeted by a power can deny it, unless it has no target in which case it is the closest player to the caster.

I would apply one d6 roll to form the pools for every player on the table.

If you're talking about games with multiple players per team, then I would suggest that the organiser would need to do a bit of house ruling.

My suggestion would be to roll a single D6 as normal and distribute that amongst the players (or, at least, the ones who are taking part in the phase). Each player then generates his own WC pool and rolls his own psychic/deny tests.

You could also work out a system of "sharing" your WC pool, to help cover players with no psykers of their own for defence.

That seems like the easiest and fairest way to handle the psychic phase in larger games to me.