When thoughts come while you are meditating, let them come; there's no need to regard them as your enemies. When they arise, relax in their arising. On the other hand, if they don’t arise, don't be nervously wondering whether or not they will. Just rest in their absence. If big, well-defined thoughts suddenly appear during your meditation, it is easy to recognize them. But when slight, subtle movements occur, it is hard to realize that they are there until much later.
This is what we call namtok wogyu, the undercurrent of mental wandering. This is the thief of your meditation, so it is important for you to keep a close watch. If you can be constantly mindful, both in meditation and afterward, when you are eating, sleeping, walking, or sitting, that's it – you've got it right!
Source: Dudjom Rinpoche from the book "Counsels from My Heart"