Should I include the proposed method name in manuscript Keywords section?
If the method is important to your work (e.g. if the method has a "blind spot" so the results might have a loophole) then yes, include it as a keyword.

As for whether to use the full name or the acronym, either is fine. When the template says "3-6 keywords", chances are very good that each group of words is one keyword. For example, "United States" would be one keyword, even though it's two English words.