How to Select a Polygon beneath another Polygon in QGIS 2.14
If there are only two polygons you can do it rather easily by selecting first the both polygons with the selection tool and then deselecting the outer polygon.
Two polygons
Both selected, press Ctrl-button down for deselecting the outer polygon
Result: only the inner polygon stays selected.
It would make working easier if the selection color could be configured semi-transparent because now the fill color is hiding the borders of the polygon that is behind. But this method does not work if there can be more that two polygons which are covering each other.
Perhaps you should make a feature request and ask QGIS developers to implement same kind of tool than the Select MultiItems tool in OpenJUMP.
In this example there are three polygons in a pile.
The Select MultiItems tools shows the list of features which were found below the cursor and user can select with check boxes which features get selected on the map. "Validate" confirms the selection and closes the tool.
If you use the Identify Features button and click on a point where multiple polygons are present, you can right-click the attribute of the polygon underneath from the list and select Toggle feature selection. The polygon should now be selected:
