It is true that often our intentions are clouded, not always so wise. If you are not enlightened yet that is going to be the case. In which case though, if you look at your intentions you may see all the positive side and you may see some of the negative side. Then depending on how Mara wants to work, Mara may throw in a few more which wisdom then has try to defeat. So yes, you might see quite a few different aspects of your intention. I would say there are more aspects rather than layers to our intentions, not as if one is above the other but rather they are kind of mixed together.
Now how can you be sure what your intentions truly are? Some people aren't always so sure. Discuss it with somebody you feel is wiser, a Kalyanamitta, to make sure you have a right intention. If you do feel you have a right intention, then you can be sure of what your intention actually is. If you feel your intention isn't so right, isn't so correct and proper, then you may be confused about what your intention really is. So if your intention actually shows itself as being right and proper, then you can feel comfortable, "Yes, that is my intention". But when you see that parts of your intention aren't so wise, then you may not want to identity with that. So to make sure your intentions are truly what they are, you have to make sure that your intentions are Right Intentions.