The middle vertical GPU mount will work just fine for a 2-slot GPU and that's what I'd recommend you do if possible. There's enough space between the GPU and the motherboard that you won't have to worry about headers.
The SSDs won't fit though.
These inner mounts should work well for air cooled GPUs in a vertical mount - certainly better than if they were pressed against the glass. Assuming that you don't have a radiator in front and only fans, the GPU will get direct airflow here as well. This should bode well for GPU temps.
One more thing about these inner mounts - you won't be able to use any PCIe Add In Cards. You might be able to squeeze somethin super-small in but it wouldn't have any braces (no available horizontal slots).
The last bit to mention about this - the thumbscrews that the case comes with do not fit on the vertical mount. You'll have to use standard motherboard screws to scew in the GPU in either of the mounting positions. Fortunately, you'll have plenty of them in the box.