Thinking about thinking

Stop for a moment and focus on breathing normally, in and out.  Can you continue to breathe normally while consciously thinking about it?  How about blinking?

The science is that these are both things our bodies do with no conscious effort on our part, when our conscious minds try to take over they can - but not as effectively as our subconscious.  There are many bodily functions that happen like this, including swallowing and shivering.  There are also functions can't be taken over by our conscious though no matter how much we try including sneezing, yawning and the beating of our heart.

I was recently caught up in an argument about whether thinking falls into the former or latter group (because apparently my friends are even more ridiculous than I am) and this led me to a startling discovery:  Thinking about thinking hurts my brain.

Before I explain the arguments, I feel I should point out that the question of how much the observer changes the observed looms large over this discussion.  When you (as observer) try and understand the way you (the observed) thinks, you can't help but be aware that you are observing yourself thinking thus negating the value of the observation in the first place because you can't be sure that the knowledge of the observation isn't having an effect on how you're thinking.

It's generally about this point that this happens:

Source

If, however, you've managed to understand everything so far then you're a) doing better than me and b) probably some sort of genius philosopher.

So the first side of this debate claims that the very fact that you can turn your thinking on itself and try to understand the way you think is proof that you can consciously control your thinking.  Fair point.

The other side of this debate claims that the process of thinking is still happening without you being aware of it and what you are thinking about is the progression of thoughts rather than the thinking itself.  Also fair point.

The response to this is that the awareness of the difference between thinking and thought demonstrates that thinking is what is being thought about, but this is rebutted by the fact that this difference is a thought itself.

From this point the argument gets into circular logic with both arguments supporting each other and there aren't enough gifs in the world to illustrate my confusion whenever this happens.

If you know the answer, or can explain this back to me in simpler terms, then please put me out of my misery!