You can pause, but that can sometimes interrupt of the flow of the story - in my experience. Are you using Audacity? If so, you can either silence the breath out entirely under "Generate --> Silence" or you can use the "Amplify" effect. It lets you amplify or de-amplify a sound, by putting in a positive or negative dB value.

Lulza just made a new post called "Podficcing: Beyong the Basics" Maybe something in there will help you?