Craig,
A couple years ago Des aka MR HG made some real good posts about shooting over dogs and desensitizing them to being shot around. The #1 thing I picked up was to shoot a small caliber gun during feeding time. Might be worth searching some of his old posts.
Last year I shot at a couple porcipines while hunting. Two of my dogs loaded up on the mule and they were done hunting. I mean DONE!
Fast forward to this year, I had a couple dogs staked out at Jesse Paul's place ( one of them was the same dog from last year), we were sighting in a 22 hornet before a hunt. The dogs did not seem to concerned. The next day, we had a small boar hog bayed in a cedar pile. He walked up and shot the hog with a 30/30 and it didn't phase the dogs, they just piled on the hog. Hopefully this weekend we'll get to see how they handle being shot over again.
I have only shot over bird dogs. But even they should be eased in. I have seen idiots work on a dog but never expose the dog to shooting. The first shot is a 12GA just over their head and they think they got a bad dog. Bird dogs I start with a 22 about 50 yards away and then feed them. I change distance and then move to larger guns. But do most work with a 22 because it is cheaper. But they should also hear the gun you hunt with many time before hunting. Doing right before feeding is easy and throw some extra petting in. You get the idea.