You can actually use ModernMix to make the apps start in window on the desktop vs opening full screen. That way you can avoid going back to the ModernUI.
You can avoid using the apps, but I think it's probably better if you just windowed them completely.
Check this screenshot for an example:
http://screencast.com/t/bpgxIuG4uKsr
And check this one too
http://screencast.com/t/wPrFXAOa
From those, I believe you should be able to get modern apps in windowed modes. In the second screenshot you can right click the apps and tell it how you want to see it.
Hope it helps!
