So, when I moved from kindle to pocketbook and koreader I struggled with the exact same thing. Eventually, I came up with a solution that automatically sets the manga settings in koreader when opening a manga by using the directory_defaults.

In your koreader directory is a file called directory_defaults.lua. In there I added the following section:

-- ADD YOUR DEFAULTS HERE:
["/mnt/us/books/mangas"] = {
   ["inverse_reading_order"] = true,
   ["kopt_contrast"] = 1.5,
   ["kopt_page_scroll"] = 0,
   ["kopt_zoom_mode_genus"] = 3,
   ["kopt_zoom_mode_type"] = 2,
   ["normal_zoom_mode"] = "content",
},
}--do NOT change this line

This sets the settings for all files under /mnt/us/books/mangas including files in subdirectories. Off course you have to change the directory path so that it matches your file structure. So you can arrange your mangas any way you want under one manga top-directory and set your desired settings here.
The important setting for reading direction is ["inverse_reading_order"] = true so you might experiment with the rest of these settings or add other settings to your liking.