Katherine, you have asked a 64-dollar question...because the source of our thoughts has to do with the nature of consciousness - which Western science has avoided studying, for the most part.
Here is what I myself do, it's something influenced by my Buddhist studies: first I look at my thoughts to see if they are wholesome, leading to health, peace, etc. (also to include fun, creativity, sense of humour...things like that). Then, sometimes I can myself figure out something about the source and decide upon more or less of that kind of thing!