I have a chestnut thoroughbred, gelding. He’s always had back issues but with proper fitting saddles he’s been doing really well.
He’s had chiro and massage, and is usually massaged once a month. He has a phantom back pain at this point. I’ve had vets look at him, the massage therapist says he’s fine and that he does get sore from time to time with our work schedule.
I agree that first you find a saddle that fits, but some times there are days where they can be a little off. My guy had a break out of heat hives a few weeks ago, I’ve had a massage therapist out twice since they have gone down and he is STILL sore. Its not a saddle issue, I have 2 new saddles made for him.
Some times you need a pad to just ease them.
I like the Ecogold pads, as their “half pad” is practically build into the saddle pad, its less bulky, and doesn’t effect the saddle fit like a thinline or ogilvy would.
I have also purchased one of these in the past http://www.amazon.com/Intrepid-International-Fitted-Gel-Half/dp/B003UT6JDU it’s great for spreading the weight out easily. When he’s feeling more sensitive than usual then I put it on.
My guy used to sit down in the gross ties, I bought him off the track and he was a wreck. Over time he’s really come a long way. He’s maintained well and he is well suited up with tack. So yes I agree with others that instantly jump on the saddle fit, but some time you have a sensitive sally that just needs that little bit more of cushion. 
Good luck.