You can just loop through layers that you want to include in the hit test and combine results from them. It's often useful to add the layer information to the results that tells what layer the feature was in.
We don't really have "out of the box popup" but there is all pieces to create one. To show the popup in the specific location see sample MapOverlays. If you want to add features attributes to the popup, you can just add FeatureDataForm control into it. Check it's properties to see how you can control it's behavior.
If you are using MVVM, note that popups are living outside of maps VisualTree so DataContext is not derived to it automatically but you can fix that by setting it's DataContext manually in view's codebehind. This is similar behavior to appbar and popups in general.
