practicing breathing through the diaphragm will give you better breath control with singing so I imagine it must work for flute, too.

One way to get a good sense of this is to lie on your back on the floor. Place your knees halfway up with and slightly apart wth your feet on the floor (yes, you may feel like you are in a Lamaze class) and as you do so press your lower back to the floor. (You can do this without bending your knees but it is harder).

Now, try singing in this position. The ONLY way you can breathe is by using the diaphragm and stomach muscles to do so. Get a feel for where these muscles are and practice tightening them and breathing through them while standing and playing. This is counter-intuitive if you breathe "with your shoulders" (i.e. your shoulders go up as you inhale) as many people do. It takes time to unlearn our usual habits. A vocal insructor can show you this technique in a more hands-on way.