Yes, you should tell your instructor about ANY injury you sustain - even if not martial arts related.
What you REALLY should do is see an orthopedic surgeon who can evaluate and identify your injury with certainty.
A physical therapist will be able to give you exercises that can help rehabilitate your shoulder, a chiropractor can tell you if your skeletal structure needs to be realigned and can accomplish more for you if she or he practices Applied Kinesiology. Those folks are rare, though.
If rest and therapy doesn't help, you need to see a sports medicine doctor - called an orthopedic surgeon. He would probably take X-rays and maybe an MRI. Most folks would see him first, but I don't know what your insurance is like or if you have any.
Since I don't know exactly what your injury is, there is no way I can say anyone or anything can make sure your injury doesn't happen again - no one can say that, really. The best you can hope for is a complete recovery and a preventative maintenance schedule - none of that can happen without some kind of attention to it.
Here's some general pointers for injuries - most of them you want to ice right away or as soon as humanly possible. I don't ice mine like everyone else - I put the ice on until 10-15 minutes after the area has become numb. I use TigerBalm and White Flower Oil. I have never tried Shengesui (sp?), but I understand it works well also. If memory serves, each one of these balms/liniments addresses forms of tissue. I think TigerBalm addresses soft tissue, WFO connective or firmer tissues, and SS even firmer tissues, but I'm not 100% sure - will find out and re-post. So keep that stuff around if you can. If you're not sure where to buy some, ask your teacher, he or she will know.
In the meantime, REST YOUR SHOULDER!!!! COMPLETELY!!!!