This confused me at first too - having just installed ModernMix, I was expecting to be able to open modern apps either from ModernMix, or the Start8 menu, or the desktop, but they didn't appear there.
It wasn't made clear that you have to go to the Windows 8 Start screen to launch them first, and then you can pin them to the taskbar or put shortcuts on the desktop or Start8 menu.
No problem really, but it would be nice if the ModernMix interface listed the modern apps available and gave the option to put a shortcut on the desktop, or the Start8 menu, or pin to the taskbar.
Having said that, it works great for me. It's kind of sad how much effort is needed to make Windows 8 work with the desktop as the main screen. Microsoft could have simply made it an option - 'Retro' or something 