Quite often bosses are not experienced in the field in which they manage, seen it numerous times they are fresh uni grads in some unrelated subject.
Your relationship should be about cooperating and understanding. Often managers are crap at explaining why they want something. Sometimes they are unaware and need educating.
If you approach them with confidence in a cooperative manner you may find they change their minds or they may give you the background that explains their decision.
Many times I've challenged bosses and been thanked for it, it's a tricky one as you don't want them to feel like you are trying to undermine them, rather help them.
I've always found if you go in with a better, cheaper, easier solution then you will become a more valued employee.
If you go in just saying it can't be done, isn't needed or that your manager is wrong then expect push back.
Don't ever challenge a boss in front of others unless invited to do so, that never ends well.
A good boss is interested in making your life as easy as possible, this way you get more done.
A bad boss is about using their position to salve some personal insecurities, these are almost impossible to please so best not to try, keep your head down and nose clean and stay off their radar.
Managing managers is a valuable skill to develope, that doesn't mean playing them rather understanding their needs and trying to fulfil them.