Not quite sure what you mean by replacing the compartments. Basically the ship is now properly upright and you can see it all at once through a 3 storey glass window. All the pipework etc has been removed so you are looking directly at the interior of the ship. It's all original wood except in a few cases where timber bracing has been installed to support some of the deck planking.
Just like looking at a cutaway drawing really. Of course, on your side of the window away from the ship, the various compartments have been recreated on three levels using artifacts recovered from the wreck so you have a sort of mirror image - on one side the reconstructed compartments, on the other the real ship. Plus of course the surrounding rooms have fascinating conserved items from the wreck, including some of the original crew where the skull has been reconstructed to show what they looked like in life.
When you recall what it all looked like when they originally recovered the Mary Rose it really is amazing what has been achieved.
Apparently, during dredging for the new carriers they discovered the bow of the ship which was missing and I believe there are plans to bring that up too although it could be 30 years before they are able to stick it on the rest of the vessel!
Colin