replacing damaged subfloor

Hi all, when my wife and I married we moved into her townhouse. Shortly after that we moved to our new home and rented out the townhouse. Ten years later our renter has moved out. I removed all the carpet and the two dogs that her live-in boyfriend brought into the house have left urine stains that have soaked into the subfloor in the upstairs hallway and one other room has an area that is about 5' by 5' in the middle that is also bad (the edgeing of the plywood is warped at the edge and the pading was stuck to the area. Anyway, I need some advice on replacing this subfloor - it is laid down in multiple sections of varying sizes - are the studs ontop of the sub floor at the wall or can the molding be removed and a section pulled out? There are also areas in the hallway where it looks like the pieces of subfloor were not laid down flush by the original builder and a leveling compound (which is now breaking up was used to level it at the joints. Is this just 3/4 plywood on top of studs? I have so many questions and so few answers. Just a place to start would be helpful. thanks for taking to time the read my wordy post.
:confused1:
Steve