You are working with two separate light sources -- your flash, and the ambient light. The exposure of your flash is controlled solely by the ISO and aperture settings on your camera -- the shutter speed doesn't affect the flash exposure as long as you are under the maximum sync speed.
The ambient light exposure, however, is controlled by all three exposure variables -- ISO, aperture, and shutter speed. Changing any one of them will affect the light seen through the windows. But -- and this is the crucial thing -- TWO of those variables are fixed by your flash exposure. The only one left that you can use to adjust the ambient light exposure is your shutter speed. So you are doing the right thing to set a slower shutter speed to get the ambient light to show up.
So your choices are (1) use a long shutter speed ("dragging the shutter") and put the camera on a tripod (and ask the model to please hold still); or (2) lower your flash power, which will force you to either open the aperture or raise the ISO -- thus making the windows brighter without lowering the shutter speed.
The key is to choose flash settings that balance the flash exposure with the ambient light in whatever way is pleasing for the final image.