The lower right window is for 6X9.
This first camera shows labeled in the leather the lower right is for 6X9, the center is for a 6X6 mask.
Some have three windows, the lower right is 6X9, the center is for 6X6 and the top window is for 6X4.5 as labeled on this camera. Again this camera has all 3 windows labeled.
Others have 2 windows at the bottom, the right side is for 6X9. To shoot 6X4.5 you align the first frame in the right window, then advance the same frame number on the backing to the left window.
On any of these types, without a mask to shoot the full 6X9, only use the right side lower window and ignore any others. Again to be clear, you must have the masks that fit in the film gate to use formats other than 6X9.
For folks with a 6X4.5 camera, many have 2 windows and like the 6X9 models that have masks for 6X4.5, you advance the film till you see the frame number in the first window, then wind till you see the same frame number in the next window.