How can I level a floor with uneven joists?
Egads. Why would you not fix the framing properly? By leaving gaps between your new underlayment and the subfloor you allow much more flex (and possibly noise) than you have now.

I'd sister 2x4s to the sides of your joists on plane where needed. Run drylines across the floor at intervals, one pencil thickness above the high points in the joists. Make additional level adjustments if things are tilted. Set your new lumber using a pencil as a spacer. 

Use construction adhesive and framing nails or gold screws to attach the lumber and prevent squeaks. Lay your new subfloor and underlayment. (I'd recommend 3/4" tongue-and-groove BC plywood or OSB, then 1/4" birch plywood.)