In time you'll get both better gear to alleviate this problem, and learn to anticipate incoming damage on tanks so you can better manage all of these resources. And yes, we have two. No, it's not hard. And I doubt, ultimately, the three you have is vastly more difficult. You're just not used to it.
I've played everything but a lock over the years, including after the big changes in Cata, and I can honestly say that, yes, while it's new and I"m learning, the 3 pools are definitely more complicated. Not rocket science complicated, no, but there's a constant lower-level conversation I have to have with myself while healing: do I spend mana to build chi now? Do I spend this chi I have built up, or save it for incoming spike damage? If I don't expend it, I won't build stacks of mana tea and I might run out of mana later in the fight. If I do expend it, I'll need to spend more mana to build more chi to generate more tea. And, finally, is now a good time to drink tea to get mana back, or should I wait until later or in the next fight?
It's a surprisingly complicated series of little decisions that add up in a big way and pretty much defines the mistweaver spec. The best monk healers will be those who master the interplay between the three resources. I'm definitely not there yet.