You can take your choice.
There are differences. The PRT program is very much geared towards doubt and fear primarily. It is the basis for Allan Gordon’s book The Way Out.
The SEP program is much more along the lines of Dr. Schubiners work - a little less about fear, and more centered with Sarno’s books. More self discovery via journalling. A lot more reading (much of the reading uses the PRT content).
No matter what you choose, realize that some reading, listening and activities are long. You can break these up. It’s recommended to do about an hr. of this work per day. Some of the lessons, reading, listening were taking me hours.. so I started to break up the days.
I did the PRT program first myself, as fear and many tms-y personality traits are covered. However I felt the need to go deeper and to have a way to make myself journal (which, you don’t need to if you really hate it) so I am now doing the SEP. You also don’t need to do both programs.
Basically each program uses different methods to help you through self discovery. The most important thing is to pick one program, stick with it and see what you like about it. After you finish the program you can continue using the skills you like for your own continued healing and self-care/self-discovery.
Enjoy your self-discovery!