Here's an example of a mixed Aperture II/GIK configuration designed to deal with a host of speaker boundary interference and related issues presented by my bedroom system's listening environment. A pair of Apertures grace the center of the front wall, and a single Aperture is installed at each first reflection point (the one on the right side is shown here).
Note that the front-wall pair of Apertures replaced three 2'x4' GIK panels--one at wall center and one behind each speaker, with noticeably improved results.
If you're restricted to starting with two Apertures, you might want to experiment by starting with one each at the reflection points and after listening to that configuration, move one each to the wall behind each speaker and see/hear which placement works better in your listening room..