Agreed, it doesnt feel "right" when you are making it, but you are doing it correctly. If you turn your square sidewayts so it is a diamond, with teh corner stones on the left and right, this is how your runner will finish up.
The little green bits that are top and bottom will be trimmed off before you add a boarder, if you want to!
I have made 2 of these, and it feels so wrong when sewing it together, but you are doing it right! LAyer your nxt colour at the cornerstone ends, begin sewing from the cornerstone end.
You are doing well!