Depends on the system really, I believe. In a 4-5-1 the problem isn't really accomadating Cahill and Fellaini, but the lack of a deep lying midfielder.
Think if we play like this:
............Fellaini....Rodwell/Castillo/newDM
Arteta.....................................Pienaar
.....................Cahill.............................
It should be possible to fit both players in.
However, in a 4-4-2 it's much more difficult, as I believe Cahill and Fellaini as a central midfield pairing, don't offer enough protection to the back four. So, and it pains me to say, as I'm a very big fan of Tiny Tim, in a 4-4-2 I'd opt for Fellaini, as I think he's better equipped to play in that system.