Dear ivac_d,
My thinking is,Those are same thoughts. Only,of some You are aware,of others,You are not. We cannot be aware of every thought,coz they are many,constantly changing,it is a mind flow,thoughts flow. You only can be aware of them,and that is the point in the first place. To see that You are aware,and that You are not the thoughts. So You keep coming back on that One Who is aware of them.
You said,'they sometimes don't seem like they are because they just rise automatically.',and that is the whole point,they arise by themself and You are apart from them. You stay with that Watcher,Witness,Awareness,or Your own Being,sense and knowledge I Am.
This is only my own thinking,so best is to find what Bhagavan tells about selfinquiry and Self Abindance. You can find that on David Godman's site,or on Realisation.org where is clear explaned what is real selfenquiry and how to do it. Sure,You can find all that in Bhagavan books,but i gave You site coz i found there very good explanation. Here is the link:
http://www.realization.org/page/topics/self_inquiry.htm
Wish You the Very Best!