Ok I figured it out. I'm using 7zip to compress the files, so that was right, but I was compressing the wrong folders. I was confused since selecting all the chapters and zipping those resulted in a single file so I was doing that, but I needed to zip the root manga folder. Your reply did help me figure that out so thank you.
Your right though, a guide would probably be a good idea. It's mostly easy to figure everything out but if you miss something it's hard to figure out exactly why your conversion didn't turn out right.