It's impossible to say where Negredo would fit in. There are very few positions where we can fill in the starters and anywhere upfront it's rather impossible. There will be rotation, yet not as much and as unpredictable as Mancini did.
Negredo imho would feel most comfortable in a 4-3-3 with Navas on the right and Jovetic coming in from deep on the lefthand side, with both Aguero and Silva popping up behind Negredo.
Either Yaya or Fernandinho need to cover defensively in midfield. My guess is the latter to be more suitable in that role.