Larger mana pool means more mana gained from innervate. Yes you would want to stack the cooldowns whenever possible, not sure why you would even question that. In the same regard however you could also tie it to throughput cooldowns such as Tranquility and Tree of Life as the intellect buff would greatly increase the throughput.
I'm not exactly sure why you are asking this question. Stacking cooldowns which complement each other is always a good idea. In the manner of Innervate specifically though the only thing you don't want is to waste mana by exceeding your normal cap and losing it when the buff fades.
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