A patient comes in with knee pain -- do I treat the knee or the hip and ankle? Someone else presents with heel pain -- do I work on the foot or everything else up the chain? What about someone with elbow pain? -- do I assess the elbow or the wrist and shoulder? As a physiotherapist, I see a lot of common conditions related to the distal extremities, and these are questions I ask myself all the time. Do I treat where it hurts and get temporary relief, or do I take the long route and treat all the compensating structures, which in turn, will result in longer lasting changes?
Most of the time, we get pain in a certain joint because it's being overused or not being used properly. I find that that's the case in a lot of chronic conditions and non-traumatic injuries. You may ask: why is it being overused? Usually, it's because it's compensating for problems that's going on at another joint. Back to my previous examples: people with knee pain usually have limited ankle mobility or weak hips, and the knee takes the blunt of the force; people with heel pain tend to have weak glutes (buttock muscles) which causes the calves to overwork and become tight; people with elbow pain may have weak rotator cuff muscles in the shoulder, and they compensate by overusing their wrists.
All physiotherapists practice differently... some may treat the area of pain, while others may focus on the rest of the body. As for me, I do a combination of both. First, I focus on treating the symptoms until they're management. Thereafter, I focus on correcting the cause of their issues. When a patient comes in with pain, they expect to get treatment on that specific area and obtain some pain relief, and I don't want to deny them that. Whether they want to stick around to get corrective therapy after that is up to them (since it does take patience). Another situation where I'll mainly focus on treating compensating structures is when a patient presents with pain in multiple areas of the body. In that case, there are clear signs of imbalances and compensations, and it would be much easier to fix the cause rather than treating each body part.
For acute or traumatic injuries where there is a mechanism of injury, the approach is a bit different. I'll lean more towards treating the signs and symptoms. I'll still design an exercise program to strengthen the joint above and below, but it is not my main priority.
A lot of people experience chronic or recurring aches and pains because the causes of their conditions are not addressed. When they get a flareup, they'll go for a few sessions of physio/chiro/massage, get some temporary relief, and then go about their lives only to get another setback a few months later. It's like taking pain medication... it'll help you control your symptoms, but the problem is still there. If you want your problems fixed permanently, it's important to correct their underlying causes.