Whatever you want. It won't make a difference. The one thing that happens is that you can visit marine resort (as a dungeon.)
craggy coast
you have to save the phione and beat garados
Manaphy isn't in this game he's in mystery dungeon explorers of Time & darkness or Sky
beat darkria and manaphy will jion your team and after 3 days manaphy will tell you whare mirene resort is.
you do the next day then you will go to craggy coast to get as manaphy puts it blue goomies
evolve,and recycle until you get a new place
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.
you go to surrounded sea and complete the dungeon and find an egg.at home it hatches and becomes manaphy.
you find a egg in the surronded sea and the next day it hatchs into manaphy
evolve all of your pokemon,recruit all the legendary pokemon.
Show it to Chatot in the guild.
to get manaphy you need to complete the game and after several days sunflorer will be talking about a secret island.