this is particular area of interest from me. I came from a Yogic background to Buddhism and noticed a lot of similarities but that the teachings on the chakras were missing... my personal opinion is that the Buddha was concerned primarily with liberation and teaching on & manipulation of the chakras isn't part of that path necessarily
the chakras are part of the body, and should be treated as such re: mindfulness of the body. worrying about you or anything else effecting your chakras is about as useful as worrying about catching a cold. the conscious control of an untrained person over their energy system is about as much as over your heart... nearly nothing. the idea that you may have opened, or unbalanced a chakra is strictly a product of new age bastardization & isnt (to my knowledge) found in the traditional teachings.
that being said I've found the practices extremely useful in general, as well as with my current practice. Yoga & Qigong are the most refined, and imo best, systems to study if you can find a legitimate teacher (which is hard). There are Buddhist teachers as well who teach about somatic energies and their usage, re: Thanissaro Bhikkhu, Ajahn Lee Dhammadharo, & Ajahn Succito They have, again imo, a much more practical and useful teaching on the subject than you will find otherwise.
Worrying that a thought may or negative feeling will 'infect' you is pointless. Intrusive or negative thoughts, in my experience, are much more effectively dealt with the methods taught in MN20 Vitakkasanthana Sutta: http://www.accesstoinsight.org/lib/auth ... el021.html
"It's easy for us to connect with what's wrong with us... and not so easy to feel into, or to allow us, to connect with what's right and what's good in us."