Directing your flow of energy = directing your attention. My instructors often tell us to "breathe into" a certain part of our bodies. So for instance, if we're doing a standing side bend (stand up straight, arms above head, clasp hands, and lean to one side), we're told to breathe into the side that is being lengthened in the stretch. Of course physically, the only place you can breathe into is your lungs! But if you direct your mind to certain parts of your body while simultaneously focusing on your breath, you get a more intimate sensation of what's happening in that part of your body. You don't just feel the pull of the stretch, but the expanding of your ribcage, the way all the muscles are reacting to each other and the way they start to relax and settle into the pose the longer you hold it.
Think about splits training. It HURTS LIKE HELL for the inflexible. How do you ease the pain? Breathe into it. Direct your attention to all those muscles and tendons around your groin, or in your hamstrings, and "persuade" them to give in a little, relax a little, calm down. In yoga, my teachers tell us not to run away from the pain, but to confront it with calmness, patience, and gratitude.
With vinyasa yoga - that's flowing yoga, where you don't hold the poses and stretch so much as weave them together into movement synchronized with your breath - you do sort of feel the "energy" shifting between different parts of your body as you flow through the poses. In down dog and most forward bends, the energy is in the backs of your legs, your glutes, and your sacrum (tailbone area). Then you flow through Plank and Low Pushup into Cobra, and the energy is in your chest pushing forward between your shoulders, your neck reaching up, your lower back crunching. With practice you can become aware of all of these sensations at once - THAT's the energy right there. Hard to explain in words, I hope that gives the gist.
Chakra yoga is not something I know a lot about, though. A couple of my teachers have touched on it but not in depth.
My massage therapist practices reiki. I'd consider myself a reiki agnostic - I don't quite buy into it, but I'm open to it in theory. Reiki is a lot about gentle touch. I think it has the effects it does not because my massage therapist is actually manipulating my energy, but that most of us are touch-deprived in some way (think about how much of your day is spent in direct physical contact with another person) and the body does respond to that physical stimulus. When she runs her hands across my body, it does almost feel like my skin is leaping up to meet her. That's the best way I can describe it - like I crave the contact with her hands. (Gosh, it's hard to talk about this stuff without sounding like a whackjob or a pervert!) She also does this thing where she places the palms of her hands flat against the bottom of my feet. I believe that in Reiki terms, this action is supposed to be drawing the energy down the channels of my body and out through my feet and, yeah, to my immense surprise as a Reiki skeptic, I did feel something - sort of a warm, tingly, sparkly feeling right in the middle of each foot.
One of my regular yoga teachers also practices Reiki and includes it in some of her classes. At the end of a very long class on Black Friday last year, I was lying on the mat in savasana (corpse pose) and she kneeled behind me and placed the heels of her hands over my eyes, her fingers on my cheeks, and held them there for several minutes. The longer she stayed there, the deeper I sank into the relaxation of savasana. Was it because of her action, or something else? I don't really know for sure. But it was nice, and I thanked her for the personal attention.
Anyway, like with most things, you do sort of have to "believe" in the woo-woo aspects of yoga and reiki to really get much out of it - but that doesn't mean they don't benefit you even if you don't believe. Even my favorite instructor sometimes says things in class that make me roll my eyes. But, you take what you can use and what makes sense to you, and discard the rest. Even in a group class setting, it's a very individual practice.