They mate. It's like how it works in real life - you don't need to put the animals in luxury in order for them to do their thing. They'll just have the intercourse.
The Pokemon that can't breed are either legendary Pokemon, or their evolutions can. If they don't fit into those categories (which I don't think they do) then Game Freak Logic.
Hope I helped. :)
Pokémon don't really breed, the Egg just "comes from nowhere", according to every daycare person ever. We an also presume that since Pokémon is primarily a kids franchise, Game Freak can't just go around making into National Geographic :)
They mate, if they do it by themselves then why do you need to put to Pokemon in the day care