OK so I added each category to the store through the multisite tool and it worked. I was hoping to be-able to use the category root to assign categories to different stores:
cateogry root -0 ->
--store 1 category root 1->
---- category 2
---- category 3
--store 2 category root 4->
---- category 5
---- category 6

Do I have to assign each store to a category?


Sorry for the triple Post but it won't let me edit!