So far so good! I was able to download it this morning.
Put it into your Apophysis file for safe keeping.
Open Apophysis and go to Options then click the Paths tab.
See the line for Export renderer. Using the little file symbol at the side of that path. navigate to where you put Flam3, and click on Flam 3 render.
Its done!
It opens a command window to render. I tried it on a small render, and it worked fine.
I found a tutorial about using Flam3 to render animations. I don't do animations, but I would love to learn how. Ignore the installation bit at the beginning, we just did that!
http://electricsheep.org/apophysis/