Jon,
I assume that you are refering to the back or cut side of the scales not being flat. You first must flatten them. Then it depends on whether or not you have a guard/bolster to say the next step. If there is no bolster, just finish both scales on the front only, then glue on one scale. Set up a jig or cradle to drill the holes perpendicular to the centerline of the blade. Drill the holes, then glue the second scale to the blade tang. Drill through the first scale holes and out the second.
Then pin and finish the profile to match the tang.
This is very sketchy, but I am trying to answer the question as direct as I can.