Me and my dad are building our own barns and...?

So I'm 13 and getting my first horse this summer. We have an old barn in our backyard but we've been fixing it up. (Fixed the ruff, put up walls, painted) Were about to put doors on the stall doors, but the floors inside of the stalls are so un even. Some start off flat and then gets higher towards the back and some start off high up and get lower towards the back. My dad thinks its a mixture of horse pee, poo, and something else like dirt that has been sitting there for a few years. (We moved in 6 years ago just started working on the barns last year) Anyways how can we even out the floor? Or we do we even have to? They won't be in the stalls that much because they'll be in the pastures but if the weather goes wrong and we have to put them in there could this hurt there back?