Eccentrics are one of the best ways to treat them. The keys are doing them heavy enough (should be high enough weight that you cannot concentrically lift it) and frequently enough (at least 5 days per week, preferably twice per day). Also it is important to try them both straight-legged and bent-kneed to see how you respond better. It is usually okay to do them when you have pain. If it is insertional, you should only go down to parallel, otherwise you can go below parallel.
Incidentally, I have come across a new technique known as "myofascial disruption technique," developed by Malcom Conway (who is a chiropractor). This is not to be confused with anything else with the word "myofascial" in it, as there are plenty of other techniques. If you can find somebody who practices it (there aren't many), I have personally found that technique to be absolutely amazing in treating many running injuries, and he claims it is very useful in bursitis and Achilles tendinopathies.
Hope that helps!