Hi Karina,
In terms of why we have two programs, this is for historical reasons. The SEP started back in 2010 when I felt that it would be nice to gather all of the free resources available into an organized program. I went through all of my TMS books and tried to take what looked like the best parts of each. Major sources included the treatment chapters in books by Dr. Sarno, Dr. Schubiner, Dr. Schechter, Dr. Clarke, and Dr. Selfridge. I also had three books on journaling, including one by the leading expert on therapeutic journaling, James Pennebaker.
The TMS Recovery program (AGTRP) started after Alan Gordon had done a number of webinars with us and wanted to tie them all together systematically, making a multimedia program. It's great because it gives you specific tools that you can use to beat TMS and decrease the underlying emotional tension that causes TMS.
Everyone is welcome to their own opinion, but my recommendation would be to do Alan's program first. (It's a little funny because I'm the guy who designed and provided most of the text for the SEP - but that's what I think.) The reason is that while the SEP provides you with a bunch of vital questions via its writing prompts, the TRP actually gives you techniques that you can apply. For example, the SEP might ask you a question like, "the most disheartening thing a doctor has told you?" This is an important thing to think about and develops emotional awareness which is a key skill in being kind to yourself and recognizing how important it is to be mindful about your thoughts.
Fundamentally, the writing prompts in the SEP are just questions like this.
The TRP is valuable in that it also gives you skills - tools that you can use. For example, it teaches you how to construct an evidence sheet, which helps you think rationally about your symptoms.
As you go through the SEP, it can be helpful to have the tools from the AGTRP at your disposal. For example, as you consider the question of the most disheartening thing that a doctor has told you, it can be helpful to know what an evidence sheet is. That way, when people tell you things that are disheartening, you can make an evidence sheet to see that you really don't need to be afraid of the disheartening things.
This is just one example among several. In general, the AGTRP gives you tools that you can apply while you do the journaling in the SEP.
That's why I generally suggest that you do the AGTRP before the SEP. However, in truth, you are welcome to do whatever you think might be most helpful.