I would probably make the attached bedrooms into a quite playroom (soft quiet toys, books, blocks, etc) with new babies items (where you might change her, where she has her crib, where her layette is kept, etc) and where you and your husband have your bedroom. The boys could take the separate bedroom so that they could continue to share (I know mine would have a hard time separating after sharing a room and close sleeping quarters) and would be less interrupted/interruptive by/to the new baby and you and your husband.
For me, it was easier to have a newborn close by - especially for night feedings supplies, etc. For a small while we had an office that we turned into a nursery. We *never* used it because it wasn't as easy (for us).
Also, when your body still needs rest and to heal, your boys would be able to either play quietly near you (especially if they are feeling like being close and need extra mama time), or take rambunctiousness into the other room. I guess your 5 year old would be school aged, and perhaps away from the house...but your two year old would probably be 3 and my 3 year old certainly appreciates space to play with vigor (while my little one is finishing her nap, for example).
There's probably many ways to arrange them in a way that works best for you all. Exciting!