If you are cutting the big square @ 6 1/2" to finish at 6", then yes you are correct, the small squares should be cut 2 1/2" to lay 3 wide x 3 long & end up @ 6 1/2" as well as the big square. Hope that isn't more confusing. I am trying to say you have it correct.
It sounds like it will be so cute. Good Luck.