I'm with those who agree to always have Lily on obey, and never use macros. Macros are inefficient when doing multiple actions, and it is better to just manually input your commands, but still set your abilities in convenient locations on your cross/hotbars.

I struggled too at first with micro-managing our fairies. How I was able to adjust was by seeing their abilities as an extension of my own. IOW, the pet hotbar does not exist; It is just another one of MY hotbars. Fairy abilities that have cast times such as Whispering Dawn, I select and use while casting another spell. This is also the time that I will manually use embrace on another party member. Shadow flare, Bio II, Broil, and Miasma are all good candidates to cast to give yourself time to use a fairy CD. After some practice, it is literally no different than using any other ogcd.

What I do wish for though since I play on controller, is the option to automatically go back to the previous hotbar set after using a fairy ability. You'd think just tapping R1 to do so is very easy, and it might be for some. For me though, I find myself going to the wrong hotbar set ALL the freakin' time!