Saving method files in Quantitative Analysis

Quantitative Analysis version 12.1

When I edit a method. For example open a method file .m or .quantmethod.xml (not sure difference), append by adding compounds, and try to save as (save is usually blanked out). I always get this error: "The method [name] already exists. Please specify a different path". 

How to save methods in Quant? What are the nuances here? Doesn't seem like this should be so complicated. 

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