I can't really give a set for Phione (Considering Phione is just NOT WORTH USING), but for Manaphy, here are some sets:
The typical set: Offensive Manaphy.
Manaphy@Life Orb
Ability: Hydration (The only choice)
Tail Glow
Ice Beam
Scald
Filler Slot: Hidden Power Fire, Psychic, Energy Ball, Rain Dance.
This set is the most common set you'll see if you face a Manaphy.
Tail Glow is what makes Manaphy usable as an offensive 'mon. Getting a +3 Boost to Special Attack in a single turn is amazing, turning Manaphy's base 100 Special Attack from underwhelming to terrifying. With a maxed Special Attack stat, this takes Manaphy's SpA up to a whopping 820. Needless to say, Scald is going to hurt. Scald is the obvious best choice for STAB, with perfect accuracy, decent power and a burn chance is always nice.
Ice Beam is mandatory coverage for a lot of Grass-types who would otherwise love to come in on Manaphy, though it also helps with those pesky Dragons, plus some flying-types.
Lastly, there are four main options for a filler slot here. Psychic deals with Mega Venusaur who would otherwise be Manaphy's worst nightmare, as well as defensive Tentacruel. Energy Ball deals with other water-types, though especially Unaware Quagsire who loves to ruin Manaphy's day. Hidden Power Fire is there to reduce those annoying Ferrothorns to a pile of ashes. Lastly, Rain Dance can be used to trigger Hydration, to deal with pesky status ailments. Speaking of Hydration, it's Manaphy's only ability choice, but it's a decent ability, especially since it makes things like Toxic, Thunder Wave and Will-O-Wisp more manageable. Energy Ball and Psyhcic also stop Volcanion from coming in and doing its best Gandalf impression (YOU SHALL NOT PASS!) by completely stonewalling Manaphy.
Nature: Modest for extra firepower, or Timid for extra speed.
EVs: Manaphy needs as much firepower as it can get for an offensive set, so 252 Special Attack EVs are a must. From there, you can be a bit more flexible in your EV builds, depending on what you want Manaphy to outspeed. But typically you should go for 252 Spd and 4 Def, to ensure you speed tie or outspeed key threats, such as Naive Kyurem-B, who would otherwise nuke Manaphy with Fusion Bolt.
There's also this set:
Cronaphy
Manaphy@Leftovers
Ability: Hydration
Nature: Bold (To deal with Physical Attacks slightly better).
Calm Mind
Rain Dance
Rest
Scald
You may notice that this set looks quite similar to Crocune, and that's because it IS similar to Crocune, except less bulky but has greater offensive presence. Naturally, Calm Mind is the crux of this set, boosting Manaphy's Special Attack up, albeit slower than Tail Glow, but it ALSO makes Manaphy bulkier. Given Manaphy's 100/100/100 bulk, not too shabby. Also of note is that Phione can also use this set, but it's inferior due to worse stats. But I digress, on with the set. You're not gonna see this one as often as Tail Glow Manaphy, but it is viable.
Rain Dance and Rest go very well together, granting Manaphy free usage of Rest without skipping turns so long as the Rain is up and it still has Hydration. Rain Dance also boosts this set's only offensive move.
That move being Scald, for obvious reasons. It has a good burn chance helping to deal with Manaphy's lower Defense stat, and it's decently powerful.
EVs are your typical Crocune fare: 252 HP, 252 Def, 4 SpD.
Just of note: this Manaphy set requires any Volcanion or other Water Absorb-wielding Pokemon gone before it can attempt to sweep, otherwise it'll get walled.
There are also some other options Manaphy can go into:
Acid Armor can be used to raise Manaphy's physical bulk, however, a physically defensive set is terrible in comparison to the Crocune-esque set.
Skill Swap can really mess up foes such as Mega Kangaskhan or Mega Mawile if they get hit on the Switch-in. It can also be used in conjunction with Regigigas or Slaking in Doubles and Triples.
Heart Swap is Manaphy's signature move, and while it's not Roar of Time levels bad, it's still pretty bad, although it does allow Manaphy to put a stop to Xerneas in the higher tiers by Heart swapping its Geomancy, if it uses Heart Swap the same turn Geomancy comes out. Most of the time, though, it's not worth it. You're better off looking elsewhere.
Heal Bell can allow Manaphy to cure its teammate's status conditions, but this has no place on any of the sets, as Manaphy has serious 4-moveslot syndrome.
You could run Physical Moves like Waterfall, U-Turn or Knock Off... I guess? It's vastly inferior to the Special Set due to Tail Glow, but you could still try it if you really wanted to.
Dazzling Gleam and Shadow Ball serve as alternatives to Ice Beam and Psychic if you want more neutral coverage, but you lose the ability to hit a lot of threats super effectively. In the end, not quite worth it. I guess Shadow Ball hits Empoleon neutrally?
