Canker sores ARE herpes; they are the Herpes-Simplex 1 virus. They belong with the same family as canker sores. My husband and I have had lots and lots and lots and lots... well, just lots and lots of issues with canker sores/HSV-1 and, after asking doctors in the allopathic community and in the alternative care community, the consensus that finally came back--from all the doctors--is that, canker sores are herpes. Sorry. That's a fact.
My husband gets them really, really bad in his mouth. We discovered that he is allergic to sodium lauryl sulfate, the ingredient that makes toothpaste foam. Once he quit using commercial/over-the-counter brands that had that and started using organic toothpaste/toothpaste without sodium lauryl sulfate, the number of canker sores he'd get dramatically dropped. Some toothpaste ideas (Whole Foods, Co-op stores, alternative health pharmacies) include: Weleda brand (there's 3 different flavors) and Neem Toothpaste (cinnamon is my fav! It can be found at Whole Foods). I love the Neem Toothpaste because it still foams; they use a coconut byproduct.
I don't really have an answer as to what to put on them inside the mouth.
BUT, I do have something you can do to prevent them. Buy a supplement called L-Lysine, 1,000 mg, from a company called Solaray. I have found that this supplement is THE BEST thing I have ever found to help control/prevent them. I take 3,000 mg/day, my husband takes 2,000 mg/day. The severity and the rate of infection we both have has dropped dramatically. But look for and buy only the SOLARAY brand; I haven't found any other brand that works as well as the Solaray one.
And yes, canker sores can be indicative that you could be 1) nutritionally deficient (that's me!), 2) could have an immune-compromised system (that's me!), 3) you could have food allergies/intolerances (that's me!), 4) could have Celiac disease, 4) could have gluten intolerance (has the same 300 signs and symptoms as Celiac disease, but it's not an auto immune disease like Celiac disease is.) (That's me!), or 5) you could have an overload of heavy metal toxins in your system, therefore messing up your immune system and your nutrients (that's me!).
**A caution about Tincture of Merthiolate, which one poster recommended. Tincture of Merthiolate (if one can even get this yet) contains Mercury. Mercury is a Heavy Metal/Toxin and shouldn't be taken. By anyone. Period.