• Awakening spell has a relatively low AP cost and clears combos and stun in a cross shape in your formation (after level 50, before level 50 it clears a row).
• Being a spellcaster, is affected by the Exorcist's Speed Cast ability, allowing it to gain AP very quickly.
• Being able to remove stuns from your team makes it pretty much the most important mercenary in any formation – a staple of any moderately serious PvP build (and most PvE builds, too).
• Holy Guard prevents an entire row from being affected by magic spells and also strips any debuffs already present on the mercenaries it affects.
• Protect, its most basic skill, is a passive skill that increases your main character's defense (up to about ~1300 at level 60 when your Monk is high level) and heals him every turn.
• Shield of Protection is like Protect, and is another passive skill that increases your main character's defense and heals them every time they are struck in combat.

Cons:

• Protect is somewhat mana-intensive outside of combat, meaning that your Monk will be going through potions rather often.
• Will find itself very often having to constantly use Awakening on itself against teams that pressure for stuns.
• Holy Guard prevents heals on your characters as much as it prevents damaging skills from landing, even if Holy Guard does heal your characters a very small amount per turn.

Abilities:

• Protect: Targets main only, raises defense and heals at the beginning of every round. Passive. (10/10)
• Shield of Protection: Targets main only, raise defense and heal whenever target is attacked. Passive. (7/10)
• Awakening: Row affect (before level 50 upgrade) or cross line (after level 50 upgrade), reduces the stun counter and awakens stunned allies. 75 AP Cost. (10/10)
• Holy Guard: Row affect, prevents mercenaries from being affected by any magic. 150 AP Cost. (8/10)

Breakdown:

The Atlantica Monk is quite literally the most important part of any formation. The ability to use Holy Guard to remove and prevent debuffs and damage for some turns is vital, as is the ability to use Awakening to remove stuns from your own mercenaries. This is to say nothing about the huge defense boost and bit of healing that they award to your main mercenary with Protect at the beginning of every turn. Healing which also stacks with a Prophet's or Princess' or Exorcist's healing, should you have any of those and be running a main of the respective class.
Shield of Protection, the other passive skill the Monk gains, is a little bit unusual. As of right now, it apparently is not working quite as intended as it drains a bit more mana than it should. Even so, it's relatively useful in situations where your main may be getting hit often for low amounts of damage, such as a ranged mercenary that gets hit at the middle or back line by cannons or guns: the amount of healing it does tends to do quite often makes the amount of total damage you take from cannons or guns very, very small. Even with that, however, it's not a very popular choice among monks and could probably use some revising and re-tooling.

As for skill assignment? For the most part, this is all up to taste. I personally recommend using Protect 60 as I am the kind of person who likes having the best possible amount of healing and defense possible from my Monk, but your mileage may vary. People seem to be comfortable simply raising it to about 40. Holy Guard only needs to be 20, but it heals more every turn when you have it at higher levels, which may make it a little more attractive to you. Awakening should at least be 21 so that it can fully clear combos leading to stun, but more is recommended as Awakening also has a secondary use as an emergency spot heal, as the more levels it has increases the amount of healing it does.