Thank you to everyone who responded. I guess I should clarify...
When I say he's a "master manipulator", I mean to a degree that is far beyond the day-to-day human nature things we do to get our way and/or keep things running smoothly. I only became aware of this side of him as he began to trust me enough to let me in on some of the secrets. I see it in action sometimes with other people when I am "privy to the truth", so to speak, and he will sometimes point-blank tell me what "projects he is working on". Even to this day, when I catch him manipulating me, it is a manipulation that has been months (if not years) in the works before I've realized I'm being manipulated. I say it will cause a fight if I mention it, not because he doesn't care about my opinion, but because he expects me to trust him and becomes offended if I do not. In fairness to him, like I said, it has not come to negative ends. But when you realize that you have been pushed into a certain behavior or situation through long-term manipulation, even if the outcome is good, it is still bewildering. It often makes me feel naive, oblivious, or stupid for "falling for it". So I guess that's where the moral conundrum ends up. So let me rephrase the question. Assuming that this manipulation continues to be used for purposes of good (to the best of my understanding), would it be wise for me to modify my attitude (both towards him and myself) to accommodate this, or am I right to be suspicious and squirmy about the fact that I can never be sure what is true and where he is leading me?