apophysis comes packaged with a variety of good basic scripts and a good introduction to scripts and scripting in apo can be found here on the apophysis main site (unfortunately i don't know who wrote it but i found it very useful in understanding the basics of scripting) and they're stored in it's script folder, in windows machines the path to this would be /win/Program Files/Apophysis 2.0 and this folder would be where you'd save downloaded scripts to.
run you scripts from the main toolbar. apophysis always loads with the 'animate.asc' script as default, running this will open up a small preview pane where you can see the flame animate.
i've found it useful to edit the animate script to read at the bottom 'UpDateFlame : False;' to edit a script open it up as shown in the above picture, type in your changes and then save using the save (floppy disc) icon. it's also a good idea to save your edited script with a slightly differnt file name so as not to corrupt your orginal script.
load scripts by selecting 'open' from the main window a lot of people have written scripts for use with apo and with time i'm hoping to create a list of soon.