I generally always have my fairies on Obey and Follow and only place them when it is absolutely necessary, like in A4 when healers have to split from the rest of the party.
Macros are a SCH's best friend. :-D
I have two versions of all my single-target healing spells, a normal-version and a macroed-version with Embrace on them, if a target needs more heals.
I also have Embrace on my normal pad, just in case. You can only have one Fairy's version of it but it works for both of them, you just won't get the cooldown.
Also, learn to switch between pads by hold the trigger button and pressing the corresponding button for that set.