That is the way Shakespeare wrote it, m-a-n-n-e-r, not m-a-n-o-r.
The phrase occurs in Hamlet, Act 1, scene 4. The friends of Hamlet are amazed at hearing a flourish of drums and trumpets at midnight and ask him the meaning of it.
He says that it is a royal drinking custom, “But to my mind, though I am native here and to the manner born, it is a custom more honored in the breach than the observance.”
In other words, when you use the phrase, bear in mind that it refers to a habit or practice, a custom of the people; it has nothing to do with rank or aristocracy or high estate, as would be implied by the word “manor.”