Hi MTL_Jon,
There is no right or wrong way to do this work, and there is no right or wrong choice if you do one or both of our free programs. Thinking that you might be doing this work "wrong" is, in fact, a symptom of the perfectionism that plagues the TMS personality.
The work is going to be different for every person who does it! You have to trust your instincts, be willing to push yourself, take some risks, and above all be rigorously honest with yourself as you do the work - that's what is required for success. You have to be able to not do it "perfectly" or and you really can't expect any kind of linear results.
Here's the specific deal regarding the SEP vs. Alans' RP: The Structured Educational Program was developed by the founding volunteers of this forum before 2011. Alan developed his own program and very generously donated it to tmswiki.org a number of years later (I can't even remember when, but not that long ago). They are different in their approach, but the goal is the same. Many people have done both.
I did the SEP in 2011 long before we had Alan's program, and I've thought about doing his program, but haven't gotten around to it, even though Alan is AWESOME and he did a couple of webinars for us back in the day, which I found enormously helpful in my recovery process.
~Jan