ᴀɴɴᴀʙᴇʟʟᴇ

What is with me and thinking of this stuff best at 2 in the morning?
So thanks to my semi I'll pick from wherever to start reading canon review I picked up on a few other things. It doesn't clash into my old theory though so it seems I'll be sticking to this theory for quite sometime now.
Now...I have a few questions:

I was reading Cheshires Arc when I noticed that Jack tend to separate Alice into two different people. Obviously because there is Alyss and Alice but still I find it weird since it is used at specific times. During the time when he is talking to Oz to something he would mention that Alice is a very important person to him and he will continue using Alice except in two panels:
( If only US history was as interesting as this... )

I have the oddest theory about Alice and the Will. I
 can't even fully wrap my head around this one. Somebody point out where I'm wrong...I need a canon review. Hahaha.

( This is what I get for not sleeping at 2 in the morning... )