Hi there Daniel, Im replying here as well as in your direct email to share with others who may have some of the same questions.
Regarding the breath throughout the chakra work, you should be using a long slow breath, and pranayama is a good way to keep it focused. Regarding the hooking of the breath to the pelvic floor, slightly flex the muscle between genitals and anus and as you exhale at the beginning on the practice. see the stream of energy run down your spine to connect to your pelvic floor and hook to it. From here, you are locking in prana each time you breath, and it will continue to raise upward within your chakra exercises and not be lost/waisted.
Please feel free to keep us informed here in the forums as you progress, and ask any questions you may have. This is a huge help to others who may not feel comfortable asking.
Dr. Joseph Kenneth.