I’ve been practicing my new flute A LOT lately (thanks Mr. Tipple!) and find that my biggest problem besides simply remembering the tunes I’ve learned, is getting the breathing right. If I practice at a slower tempo, clearly I don’t breathe at the same spots I would at a faster tempo, and it’s getting the breaths in that’s throwing me off most often (also the howling of my neighbor’s dog, but that’s another matter). Once I start to get a tune up to speed, I find I’m breathing at phrase points consistently, but if someone else calls the tempo, then new ones must be found. I’m often left gasping. Any suggestions, resources, etc that folks who’ve mastered this issue can offer?
there’s the huff & puff technique…rather affects yer playing style, not that that’s always bad. The trick is shifting back out of it without quiting the playing altogether.
A lot of it will get easier as you develop a better embouchure, you will simply use less air. You may also see some increase in lung capacity if you are new to wind instruments.
Being conscious of the issue and working with it is good at this stage. The biggest mistake is practicing something that you do not want to become a reflex in a few months. 
Just go on practicing, trying not to always breathe in the same moments, and listening to flute recordings to see when they breathe. It takes time…
Breathing? Now, just hold it a minute…
donna be pickin’ on the Italians
Is she? Shirley not.
Ida know…are you guys getting enough oxygen?
Well, if yoda know, who does?
Take a deeeep breath and… feel the force!
da farce boss, da farce
Wind players learn to use stomach muscles to support breathing, and I’ve always known about that, but recently I’ve been taking a vocal class from an instructor who is famous for knowing the physiology behind singing and being able to apply it to get significant improvements quickly. (Her name is Jill Jaxx.)
My take-away from her class is: keep your chest expanded. It will make you use your belly for breathing properly, but it will also let you take in more air quicker. So it’s really helped with my flute/whistle playing as well. The trick is to make it a habit.
So yes, you have to work on your phrasing and where to insert breaths, but this will give you more options because you’ll be able to make your phrases a little longer, if you choose to do so.