It takes time, time, and more time IMHO.

How many miles/hours have you put in for the last 90 days ?? It can be good to stand on the pedals for 30 seconds every 15 minutes to let blood flow back into all the stuff you sit on. Standing or at least taking some weight off your butt as you go over rough stuff helps a lot too. It is also a lot easier on your wheels, your legs act like shock absorbers kinda...and it puts the shock into your bottom bracket not higher up on the frame. I have put a lot of my miles the last 12 months around the same 22 mile loop, this let me learn where the bumps are, but after the weather last winter it looks like a minefield now.