So if I understand blue Remy was actually Apocalypse, but regular Remy is actually Remy. Whatever magic Rogue did allows regular Remy to be in control of Remy's body.

I assume the next step is exorcising Apocalypse from Remy's body. If they do nothing then Apocalypse-Remy will return.

For Warren I think he's still got a little bit of Apocalypse in him. I'm guessing it's a case where he thinks he's in control, but he could easily be overwhelmed.

I think for Apocalypse to be truly defeated Warren would have to give up the extra power he was given.