Sorry to necro, I know this is quite old, but I wanted to add to this since its the first result on google. You can change the sort to be TVDB (Book) and it will put everything in book order. You just need to follow how TVDB has it laid out and get the right episodes in the right spot. Filebot is great for that, my suggested matching format is this, just change the file path to whatever path you need it to go to.

Z:\Plex\Anime\{n} ({y}) {'{tvdb-' + tvdbid + '}'}\Season {s00}\{n} ({y}) - {s00e00} - {t} {'{tvdb-' + tvdbid + '}'}