Healing is one of those questions where there really is no one "correct" way of doing it. It's all down to trial and error to find what works for you.

Personally I use a mixture of the pro-config, virtualization of healing rotations and click healing.

My DPS rotations keys (1-6) all trigger my basic healing rotation on my healers. Then I have a keybind to cycle virtualization to change that rotation to other healing rotations e.g. Slow PVE healing, AOE Spam healing, DPS Mode, etcetc.

All my healing macros are set up with 2 tiers, so that if I have a focus set on my healers, they heal the focus. If no focus is set, they mainly cast on TargetofTarget. So for a simple example:

Code:
/cast [target=focus,help] Healing Surge
/cast [target=targettarget] Healing Surge
To set focus I use a good ol' repeater region over my party/raid frame and a macro with the addon Clique. Additionally I've setup external CDs, battle-resses, normal resses, some utility, and spot healing macros to be used through click healing.

Oh, and naturally I have separate keybinds for large healing CDs like Revival, pally wings, etcetc.

I always found only a combination of all the methods was really sufficient. With doing all the healing manually it took far too much focus to do efficiently and just relying on pre-set rotations was too inefficient most of the time. This gives me a decent, flexible setup with an underlying layer of auto-heals that require no real attention, but still gives me control over the healing.