So, in the building that could be potentially be my studio, every room has windows in it. Will these mess the acoustic quality of the room up?
if you are not using high end condenser or ribbon mics you should not have any issues. Most of the studios that use these high end mics are built around being quiet and "Dead".

A home studio should not have much issue but if you are in a noisy location consider hanging heavy drapes over the windows.