I have been using Apophysis since 2005 and I don't understand it either. I do exactly what you do with the flame programs I use. I have Apophysis on one laptop, and jwildfire on another.
Since, so far as I know, Apophysis hasn't been updated in years, it may eventually not work on different or newer OS's. Just a guess. I don't really know.
There are many tutorials on dA, if you check the Apophysis group or do a search for Apophysis tutorials. I never could do them because I have learning disabilities and some things I just don't "get". I don't understand what the directions are telling me to do. Somewhere between my brain and my hands something goes amiss and what I perceive is not what the tutorial is saying. I know this because when you have that kind of a tutorial, they will show step by step a screen capture of what your workspace in Apo should look like, and mine never did. So I did just what you do. I try different stuff, tug those transforms around, resize them, try different weights, all that good stuff and see what I come up with. Even as frustrating as it is, I still love fractals, especially flame fractals. Don't give up. This is very lovely and vibrant!