Besides shorts, don't forget to stand up on the pedals and stretch with some frequency to give those sit down parts a rest and let blood circulate. You might also want to just get off the bike occasionally. If you can, push a little bit higher gear for a ways...pushing the pedals more forcefully can take a small but significant amount of weight off your sit areas. (I find light spinning recovery days harder on my butt than harder "push" days....get a little variety in the parts-that-hurt on any given ride.
I may get roasted for this, but rubbing on a litte neosporin to those crotch areas that get chaffed, both before and after a ride, also seems to help.
And finally, depending on your bike set up, you may tend to creep forward on the saddle as you ride....and riding the nose for any distance can be hard....best to move around on the saddle regularly-- eventually on longer rides, you may run out of comfortable places 8-)