CTRL-D (Database) is your friend. Dump the Pokémon you want, then they'll show up in the database.
Just run searches to find what you need, no boxes since people can have collections >10k. No need to organize or clone, everything is just data!
If you have a ton of Pokémon dumped, it'll take a while to read all the files from your hard drive. You can always open two instances of PKHeX and drag&drop between, or use the box viewer to transfer between boxes in the same save file.