The deck boards will flex and pull up against the joists when you screw them down. A little bit of un-evenness isn't unusual in any deck.
However, if you want to try to make the joist tops even, you can either re-install the joists that weren't put in with the crown up, so that all the crowns are on the top (this is the best for a floor). Or, you can add shims across any low spots as needed. If you do use shims, use cedar - it is naturally resistant to rotting.