If you want to profile your whole system under mixed-mode, you will need to create a custom analysis profile. Here are some quick steps to get you started:
Under the Analysis Target tab, choose Profile System. Then under Analysis Type, look at the last item in the tree. You should see Custom Analysis. Advanced Hotspots uses the sampling driver (hardware collection). Therefore, go ahead choose Hardware Event-Based sampling Analysis. You may wish to add any interesting events you are interested in looking at (clock ticks, instructions retired, cache misses/hits, just to name a few..).
PS: The event names are very often self explanatory, but more details can either be found in the processor manual, if you are curious. For your own convenience, VTune gives a short summary on what an event means.
Scroll the configuration window (Properties section) and towards the end, you should see Managed runtime type to analyze. Choose the runtimes relevant to your code.
This is how you can configure your mixed mode profiling.
Please let us know how it goes.