I'm sorry if this would be more suited for the Introduction To Theravada subforum.
I'm a relative beginner. I've been practicing Anapanasati for a few months, and I try to attend a meditation with a Sri Lankan bhikku once a week (metta + anapanasati). Often, while meditating, I seem to be unable to tell whether or not I'm thinking. The space seems to be empty, but I feel like there is more going on than I am aware of. Sorry, it's hard to describe... does anybody know what I'm talking about?
Also, I find it very difficult to breathe unintentionally. I begin to worry if I'm suppressing the breath intentionally, etc
The important thing is to try and not breath intentionally. It may be difficult at first but as you continue, you should relax. As far as not telling what you are thinking - its just an artefact of practice. Its nothing to be concerned about but do ensure that you are maintaining awareness of the object of meditation and to consistently apply the instructions you have been given.