Co-equal branches of government?

What is the meaning of co-equal branches of government if at a moment of Policy differences one branch decides to bypass the other branch? 

Is a campaign promise more important than the respect of a constitutional disposition? 

I disagreed with Obama bypassing congress and I will disagree with Trump bypassing congress to have his way on the wall. 

But I do want him to just do that, so we can have more arguments to remove him.

And if he does bypass Congress, the third branch of government will have to decide.