I have tried many addons for totem management and have always come back to just using the standard UI.
You can break your totems down into a couple classes.
Buffs: 5-minute duration, non-reactive; you can place these before the fight and may need to refresh them once
Counters: shorter-duration, usually reactive (think Cleansing, Tremor, Grounding). These need to be used quickly, and in reaction to an enemy.
Offensive: shorter-duration, and need to be near an enemy (think Searing, Magma)
Elemental: used infrequently, but may need to be used in an emergency (especially Earth)
The different usages suggest different ways to setting them up.
Buffs will tend to be cast once, before combat; I put my standard lineup all next to each other and just click through them.
Counters will need to be used quickly, so reaction time counts. When I'm PvPing, I have tremor and grounding on my quickbar. I keep Cleansing on ctrl-1 at all times and it's just muscle-memory now to hit it.
Offensive totems are whatever works for you. I usually keep Searing on my quickbar so I don't forget to refresh it; magma is off to the side because I don't actually use it that often.
Elementals are a tougher call -- they're on such a long cooldown that you hate to give them a really prominent place or keybinding. I keep mine at the top-right corner of my screen so it's easy to whip the mouse over and hit it if needed. (look up Fitt's Law if you're in the mood for human-computer interface geekery

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