Is a new substance automatically added to a method?

No. You have to manually add substances that you create to the method(s) you use.
We recommend making adjustments in a copy of the method(s). You can make a copy of a method by selecting it, and then clicking the 'Copy' button on the right side of the method index. A copy of the method will open. Make sure you rename it to avoid confusion with the original. Please note that the copy will be saved in the project you are currently working in.