Is there a way to "minimize" a Modern UI app to the traditional taskbar? I feel that having to manage two kind of taskbar, one horizontal and one vertical is too cumbersome. Is there a way to merge them into one so that I can better track the apps (both desktop and modern UI) that I have opened?
Pressing Alt + Tab will show a list of all of your currently running apps, regardless of whether they are Desktop apps or Modern UI apps.
As far as I know, there is not a way to pin a Metro App to the taskbar. You can pin a Desktop app to the Start Screen, but this will not show whether it is running.
If you swipe-in from the left, you will see a list of all your running apps, but "Desktop" will count as a single app, regardless of how many Desktop apps you are running. So I think Alt + Tab is the closest to what you want.