Well my best guess is that they are connected to the undersuit someway, but they aren't fused, since his armor is removeable, it can't be fused sicne he couldn't squeeze out of the suits neck hole, and Master Chief is human after all. He could gain wieght
But either way it's connected temporarily, but i don't know how for sure, sorry.
I'm not sure where it is mentioned if at all, i don't remember it mentioning how in the Fall of Reach, but i could be mistaken.
I think it's one of those things that they just don't need (for general purposes) need to get that deep into.
Cause most just play the game, and don't wonder or really care, all they know is it works. But i wish i could help. my best advice is just scan The Fall of Reach if you have it, or keep searching. But i'm sure it's not really mentioned anywhere, if it is, it's in the novels.
-Justin