You have a number of options. The frames can be used interchangeably. You can put that medium box with bees on top of two of the foundationless medium boxes. You can add the empty foundationless medium boxes on top of the box with bees. Or you can add the medium on top or the bottom of the deeps. The only issue with adding foundationless boxes on top of a box full of bees is that sometimes they are inclined to build up from the bottom of the frames, thus bypassing the guide. This can lead to crooked combs. To avoid any chance of crosscomb, you can also alternate the foundation frames with the foundationless frames. This way the bees MUST build straight combs in your foundationless frames.
I wouldn't worry about regression issues, etc.