When you pay attention to your breathing. What exactly do you do?
Many people will create tension around their eyes when they focus on anything. I guess because they created a link between the word focus and their eyes. So if that's the case see if you can relax the area around the eyes a little.

I found it helpful when working with the breath to see where in the body I tense up, where I relax etc. try and ease the tension a bit, but mainly focus on where the breath moves freely. where it's nice, comforting, filling, and easy. Then try to expand and spread that sense of ease and comfort as far and wide through the body as you can muster.

The painful and tense spots will be there for another time to deal with.
Maybe try breathing through the soles of your feet?

In the past, I have consciously closed and shut my chakra and pictured another kind of energy system. Which was helpful in maintaining some balance when my chakra work got out of whack.

What to do with chakra? Anything you want really. What do they mean to you, why would you want to open them. what do you think happens?
In my opinion, chakra are ideas that can be utilized, pictured, and used to gain certain effects. The same benefits for lack of a better word can be gained by many means. Just because the chakra system(s) have ingrained the spiritual world deeply the last few years is because they can be useful as a frame of reference. Not necessarily because everything written about them is true.

Useful certainly. necessary nope. They signify/symbolize a center between the spiritual/mind and the corporeal/matter. Throughout different cultures, many such symbols have been used as focal points.