As a project manager, in case of a conflict with your boss, what is the best way to deal with it for the best interest of all concerned?

I had a similar issue before and i come up with some points

- your boss is an important key success for your achievements so he must be satisfied or at least convinced with all what you do.

- understanding the different points of view and building a common ground will helps a lot, focus on business goals as a common point, thinking about your own goals separately will not help you at all.

- Most of project managers usually specialized with technical background and the boss is business man who deal with business you may involved in details but his vision is wider.   

In PM profession, experiencing conflict is common phenomena thus one of the important PM skills is ability to resolve conflicts.  There are many situations where our boss will not agree with our suggestion or vice-versa we do not agree with our boss decision.  In this situation as a PM we need to communicate with our boss in affirmative way and explain more details about the situation.  Some times conflicts occurred due incomplete information receives by the boss;  We need to explain pros and cons of the situation to the boss and let him know the real scenario with possible alternative resolutions,  Its difficult but not impossible to get agreed upon into common point.

best way is to convey/communicate your opinion to your Boss, but follow him keeping in mind that he is superior then you so that is why he is your Boss.

Try to not enter on direct confrontation and try to get some balance in the decisions.

If possible, like Mr  Zaferullah wrote, explain the pros and cons of such scenario situation and try to add more good values for the point of view.

First thing PM should think is how come PM cannot convinced the Boss... Look at the very detail root of the conflict.. If its technical, more or less the Boss is not satisfied with the presentation or what so ever depends on the the situation 

We cannot disregard the real attitude of each individual.. In that case, that is the PM hardest assignment. This i believe is more difficult than what you prepare for you presentation.

But still since you are already a legitimate PM there is no doubt that you cannot resolve the differences

I think whatever you take to the boss for a decision shall have options for the boss to choose from. In such cases most probably he'll agree to one of the options presented. If he doesn't agree to all the proposals then after all he's the boss. If one thinks that this difference of opinion is very critical and would affect the project badly he's got2 options: Either get the difference of opinion documented or leave the team (second option not recommended).

It is better to understand your boss view and what he is trying to convey you, We can always puts things & our concerns  in a convincing manner  before our boss with alternate solution.

Instead of posting problems on him and ask for his guidance how to go about and deal further I think that your boss will have the best solution and answer for all your problems.