Here's basically how it works.
ICSTOR comes up with a broad outline for how the next chapter in a particular girl's arc will go in an update. I believe this is actually written down and given to Onyxdime later, but it might just stay in his head.
ICSTOR then makes renders for the story as detailed in the broad outline. When these renders are done, they're sent to Onyxdime, who writes dialogue to go with each image into a script. Finally the script is sent to a coder who actually implements the script + images into a playable VN.
It makes sense to do things this way if you're an artist, not a writer, but you still want to be the one with full creative control over the story and where it goes. The main problem is, other than the constraints it puts on the writer, the other members of the team have nothing to do but sit on their hands until the renders are all done. This can be fixed to a degree with some assembly line-style production: Sending renders to the writer in bundles rather than waiting until they're all done. This is apparently what they've started doing: ICSTOR mentioned that his coder has already completed some new minigames, which implies they were sent the renders used for those games before the whole set of renders was finished.