So Shoko uses anidb to match shows. It uses the hashes anidb has of pirate/fansub releases. So anidb will not have the hashes for your own rips and Shoko will not be able to automatically match them. Your use case isn’t really what Shoko was designed for. Shoko does have the ability for you to manually match files and has tools for matching files in bulk. Shoko can solve your issue with anime with multiple seasons split into multiple entries, so manually adding everything might not be a bad idea.
I haven’t really used those much but they will probably be better at matching your stuff automatically. Although it would be to TMDB’s data. TMM can do anidb but only if you pay for pro.