Writing letters DOES help. You just need to make sure you're writing like a sensible adult. Don't go after all stores staying things like "It's cruel to keep Bettas in cups" exc. because they don't care.
What you want to do is actually tell them your first hand experiences about the neglect the fish at a particular store are going through. Take pictures. Tell employees before complaining to corporate. Once all that has been done you can then complain and tell them what the employees did (or didn't do) and about how awful the fish's conditions are. Typically they don't ask for photos but you can mention on your letter that you DO have them. Be sure to explain in detail about what you saw, use correct grammar and punctuation.
If things don't change for whatever reason do it again, you can even call and complain.