Moves

Tail Glow is the main reason to use Manaphy as it can easily boost to +3 immediately. Scald is main stab and has good neutral coverage and nifty burn chance. Ice Beam and Energy Ball provide coverage; Energy ball is can beused to hit bulky Water-types such as Rotom-w and Jellicent that can take a Scald, while Ice beam is an option to hit Grass- and Dragon-types such as latios and amoonguss. The last slot Rest grants full healing in a turn when rain is up. But if unneeded, Protect is a tried and true option to shield Manaphy in various situations.

Set Details

The given EV spread lets it outspeed neutral base 100s such as Mega Kangaskhan and maximize power, with the rest invested bulk. Wacan Berry is used to resist and KO Electric-type Pokemon such as Rotom-W or Thundurus. Sitrus Berry can be used to give it more staying power. Mystic water is an option for consistent power without recoil, but other items typically outclass it. Rindo berry is another option to live through strong grass-type attacks but they aren't as common as Electric-type attacks so it's usually not as useful as the other options.