Hi, thanks for using Zonelets!
I have replaced every "posts/" in the script with the title of the folder that my chapters are in, since it said in the file that that was something you can do
Could you possibly point me to where you're reading this? This won't work by default, so I may need to rephrase anywhere I have implied this!
With the default Zonelets script as of version 1.52, you can't easily rename the posts folder without breaking the title/date parsing. This is because it looks for the date information an exact number of characters into the url string. Also, for example, the script relies on there being only one posts folder called "posts" to make the header links work. So I think those links might break if there was a single blog with posts in multiple different folders.
The neatest and most stable method to approximate what you're trying to do is, I think, to make multiple completely separate blogs. So each story has a fresh copy of the full Zonelets folder structure. Depending on how many stories you have, it might start to feel like a silly number of blogs, but I do think it would work! You could add header links to the other stories, or back to your home page on each story's blog. On my site, for instance, there is a Zonelet within a Zonelet (see the link "Puzzle Corner" in the header)
Otherwise, it might be worth looking into other options besides Zonelets or learning some Javascript to change Zonelets to suit your needs better!