When pkm are stored in the box, their party stats are discarded in order to save space. Only 232 bytes are needed, the rest can be recreated on demand. When they are in party format, they have an extra 28 bytes at the end of the array to store party stats (current hp, stats, status affliction, etc).
EncryptedBoxData is the format a pkm is in when it does not have party stats and is encrypted.
DecryptedBoxData is the above format, without the encryption (easy to reference in a hex editor).
EncryptedPartyData is the format... when it has battle stats and is currently encrypted.
DecryptedPartyData is the format when it has battle stats and is decrypted.
Easiest to save pkm files it in the Decrypted Box format (232), since the party stats are negligible and in bulk they consume space. Decrypted because you don't need the encryption.
When PKHeX handles a PKM, it keeps it in the Decrypted Party format (260) so that if stats are required for logic, the array is ready to go.