Hey Paul, unfortunately similarly to my last sentence, you can't change the template used by these predefined templates. If you already have another template that you'd like to use, you can just create a new email in the predefined templates, or you can create a new template and then create a new email using the new template. (Sorry for the dual meaning of templates here.) This can be created in your program template so that the next time you clone the program, the new email comes along with the clone for simplicity.
While the things that implementation specialists set up are helpful for the initial stages of using Marketo, you'll likely find out that you need to branch out from what they've created, and break new ground at some point.