I don't use the stuff sacks that come with tents. Like others said, they're usually too small. Also, even if you pack the pole bag separately, those sacks usually force you to store them vertically, which isn't always practical. But most important, if it's rained during the night, using a single sack means that a relatively dry inner tent gets put into the same sack as the really wet fly. So, if you don't get to dry it during the day, the inner tent will be wet by night. Yuck.

I get two smaller stuff sacks, and store the fly in one, and the inner in the other, to solve all those problems.