Windows you could do a few things. Apply a glass or transparent texture to the windows for the glassy look... however a midevil tower style would not have glass.

You could extrude the window in slightly to give it some depth then delete the face to make it look into the room.

Or you could make the window face black.

To make it black go to hypershade, create a new lambert, set the color to black, highlight the faces you want to be black. Right click the texture and "apply to selection".

I like the work so far, looks very nice. I especially like the temple on the high ground.