Actually we don't know that, but judging from fact that Apocryph killed Cross with Judgement, Cross weapon, I believe that any Innocence listen Apocryphs orders, case he is like the one who have right given from "God", or from Heart. If you think about it, Apocryph when find out that Allen have Nea inside of him , tried to became one with Allen, to destroy Nea, or actually "supress Nea's memory". I'm not really sure here so it could be both, and maybe Apocryph was the one who give Innocence to Allen knowing that Allen have Nea inside.
Well, that's the problem. You see I believe Allen ideed have Mana inside of him. Just look on this pannel.
Here we saw how Nea took a control on Allen's body. And Nea wasn't thinking that time to give Allen his body back.
But then happen this thing, and I'm sure this is clue about what and who Allen is. In a moment when Nea's seal was broken we saw this:
As you can see Nea was represented by Allen's right eye, but then Mana show himself and break Nea's control on Allen
And this was not the first time when we saw Mana as part of Allen.
Also that was not the first time when we saw Mana like this. It happen also in Crowly arc,.
We saw Mana for sure here, he even called himself as "darkness" and the next pannel we see this
Mana here after listening Allen said that he need go deeper to a world darker then black and brighter then white.
Now you could say that it was Nea, but that the problem, Nea was supressed by "Mana". Also I really doubt that Nea know about "cursed eye", he rather was surpised to see it
So you ask, what is really happening? Well, because it was said that Nea and Mana are back side of War we could say that Mana is Darkness indeed, while Nea should be Light. So it will have sence to Mana being able to supress Nea, and Nea to supress Mana. So if person have them both inside he will be free to chose between whatever he wants and I believe that someone(maybe Past Allen) planned all this to gain both part of Nea and Mana souls. So I don't think that Mana is not inside Allen...I believe Mana is part of Allen, as well as Nea. Again Cross said that there is hidden side in this war, and it could Apocryph, but also it could be Past Allen who decided to wreak havoc things.