Hi Monica,
If you only work with one or two of the chakras, or anything less than seven, you are likely to put yourself out of balance from an energy standpoint, and maybe even cause health problems. Plus, if you do work with all seven, you get a feel for each of them and understand which one seems stronger to you and which ones don't. In future meditations, you can focus more time on the ones that seemed a little weaker, so it's a learning experience for sure.
I know that there are some who may only focus on one or two, they're not getting the full benefit from their meditations.
Take care,
Nancy Welker
Bellaonline Yoga Editor