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I put the fairy next to the tank and let her autopilot (with Eos anyway, Selene is another story)
Usually the tank is what needs the most heals but if a DPS gets knocked down, you can let the fairy do a heal on the tank while you take care of the DPS.
Some people like to micromanage their fairy but I find it tedious and almost a waste of time? In the time I'm micro managing her on & off obey I feel I could have used to do some quick DPSing to help bring the mobs down quicker. This has worked for me in every dungeon up to & including Amdapor Keep/Ifrit HM/Chimera.
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I think it just depends on what you're comfortable with... I use a Razer Naga, and have almost everything keybound to it. However the way I do things has been developed over several years of gaming, so it won't work for everyone and it's what I'm comfortable with.
I use Q and E to "Place" and "Heel" the fairies (I use my mouse to strife), and I keep "Embrace" and "Whispering Dawn" on my hotbar for spot healing. Otherwise, I just let Eos do her thing. I gave up a long time ago with trying to micro manage everything she does, because I found myself focusing more on those small things rather than healing my tank and party members. Once I've placed her, I'm happy with her spot healing the party... Others may find it wasteful of her CDs, but I feel confident enough in myself that it's not necessary to worry about her blowing them.... Would it be nice to control when I can use her skills? Absolutely. But until the pet management system is improved I'm not going to fret over it.