I know you see it when you beat the boss but later can you catch ho-oh?
Yes. It's at Mt. Battle.
Ho-Oh can be acquired at Mt. Battle by defeating all 100 Trainers in Battle Mode (either Single or Double Battle) with their Story Mode party after purifying all 48 Shadow Pokémon in Story Mode. Ho-Oh will then be placed in an open spot in the PC's Pokémon Storage.
http://bulbapedia.bulbagarden.net/wiki/Mt._Battle http://bulbapedia.bulbagarden.net/wiki/Ho-oh#Game_locations
