I didn't know what to do once I went to the Blissey Secret Base, so I made the Blissey owner my Secret Pal. Will he have a Blissey when I battle him?
If you challenge him in his Secret Base:
Yes, he will have Blissey.
If you challenge him as a Secret Pal in your Secret Base:
No, he will have the NPC Pokémon.
Source: Experience