You can just change .zip to .cbz either manually via a filebrowser or a script (cbz are essentially just zips).
I think .cbz can only contain images, no subfolders, so maybe you need to make a .cbz per chapter or do a lot of remaming to be able to put them in one directory.
Cbr is the same but for .rar files (which are not open source?).
I think there is a program for adding metadata to manga like Comictagger (which does not work too well for manga) but I can’t remember the name …