After Manaphy leaves and you beat the whole game, sleep for a few days, and Manaphy will come back and join your team.
Manaphy isn't in this game he's in mystery dungeon explorers of Time & darkness or Sky
craggy coast
you have to save the phione and beat garados
evolve all of your pokemon,recruit all the legendary pokemon.
beat darkria and manaphy will jion your team and after 3 days manaphy will tell you whare mirene resort is.
evolve,and recycle until you get a new place
Whatever you want. It won't make a difference. The one thing that happens is that you can visit marine resort (as a dungeon.)
I can't remember at what point he joins your team, but if you keep playing the story line, he will eventually join, I think.
NO
you go to surrounded sea and complete the dungeon and find an egg.at home it hatches and becomes manaphy.
Surrounded Sea
possibly anyone you see in mystery dungeon are possible to get