Mouth rot (infectious stomatitis) is generally considered to be a secondary infection...that is to say that it is usually not the main problem. While certainly things such as direct injury can lead to the development of a primary case; the usual avenue is stress, illness, suboptimal conditions, etc weakening the immune system & allowing the ulceration(s) to form & progress. When caught early, correcting the base problem and instituting corrective and supportive therapy are usually sufficient (fix the problem, increase temps, minimize stress, and treat the wounds as needed). However, as it progresses a few things happen: Frequently systemic infection builds which requires antibiotic therapy. The ulcerations advance and deepen, affecting more and more healthy tissue, and (in extreme cases) sometimes affecting bone or muscle structure. Old school treatment was varied, but often included household items such as Listerine and/or hydrogen peroxide. Both were actually of some benefit, but there are much better ways. As previously stated, the old standby - peroxide - actually damages healthy tissue as it works to slough the dead/injured cells, thus lengthening the healing process. Certain oral care solutions, dilute betadine, dilute chlorhexidine (use with care over an open wound), or antibiotic flushes are all better options. When removing caseous matter, care should be taken to ensure that neither it, or any flushing solutions are allowed to pass the glottis (go down the trachea). Personally, I recommend against letting it go down the esophagus as well.
Keep in mind that the treatment process is very stressful, and can often aggravate the condition (think: prying the mouth open generally involves putting pressure on weakened tissue, even if you avoid the injured area...AND cleaning out the wound typically means reopening it)