This is a very intriguing question! The passage you quote occurs near the very end of Chapter 32:
But I now leave my cetological System standing thus unfinished, even as the great Cathedral of Cologne was left, with the crane still standing upon the top of the uncompleted tower. For small erections may be finished by their first architects; grand ones, true ones, ever leave the copestone to posterity. God keep me from ever completing anything. This whole book is but a draught -- nay, but the draught of a draught. Oh Time, Strength, Cash, and Patience!
Moby-Dick might be called the “draught of a draught” (that is, the “draft of a draft”) in several ways.
In the first place, the novel is highly unconventional in structure, especially because of the inclusion of the lengthy, detailed account of whaling and of whales as a species. In some respects, the structure of Moby-Dick is epic or encyclopedic: it touches on a great deal that is not strictly or obviously “relevant” to the main plot, and the chapters on whales and whaling are the obvious examples.
Melville implies that he is not attempting to offer a smooth, polished, perfectly structured book. He implies that truth is complicated and ragged and cannot be fit into neat little prefabricated boxes. One’s perception of truth, he implies, is constantly evolving, especially if one has a capacious, probing, thoughtful mind, as Melville did and as Ishmael also does. The idea that the novel is merely the “draught of a draught,” then, implies Melville’s respect for, and openness to, the full and genuine complexity of reality.
At the same time, Melville realizes that he has taken on a literally gigantic task in trying to write a book such as this. He is proud of his effort, but he is also humble in his recognition that nothing constructed by man – certainly nothing as ambitious as this novel – can ever be finally perfect or completely finished. Moby-Dick is deliberately not the "final word" on anything it discusses. A man like Ahab would try to have the "final word"; a man like Ishmael would not and does not.
Indeed, if the quoted passage is seen as a reflection of the personality of Ishmael, it shows him expressing his typical humility and his typical thoughtfulness. He is well-read; he knows about both whales and cathedrals (and much else); he is constantly hungry for new knowledge; and he never assumes that at any point he has reached the complete truth about anything.
The phrase “draught of a draught” implies that the structure of Moby-Dick is a bit of an improvisation, invented as Melville went along rather than fully outlined and pre-planned before he began writing. Melville recognized that he was writing an unusual book, unlike anything, really, that had ever been written before. He recognized, too, that he was even departing from many of the more conventional structures that had made so many of his early books so successful. He knew that in writing Moby-Dick as he chose to write it, he was running the risk of producing a book that the general reading public would not comprehend or appreciate. His willingness to write such a book shows his courage, his integrity, his inventiveness, and his dedication to depicting expereience in all its messy complexity.