yeah. Same for me.
When I am using a waterproof sack, I am not using the compression stuck sack given with the bag.
However, in the summer time, when it's not really likely that it will rain, I don't use the waterproof sack.... In this case, I use the stuff sack (which is lighter). Because I don't like to think that my sleeping bag is directly in touch with the bottom of the pack (moisture, sharp rock).
Depending on the configuration of your pack, stuff sacks can be practical for a few items (food, shelter, electronics/papers)... Maybe, try first to use the various pockets of your pack in the optimal way. If you feel that you need stuff sack to organize all of that, then use it.... but if you're wondering whether or not you should use them, it's probably that you don't need them!!! :P
Rather than trying to find good reasons for taking a new item in my pack, I try to find how I could manage without it/them... =/
Keep it simple! [thumbup]
Then, with experience, I know whether or not I am ready and willing to carry the extra weight...