Twain remembers well the most valuable lesson he learned as a steamboat pilot on the Mississippi: you have to know the entire river by heart, you have to learn it like your A.B.C.
He compares the practical knowledge gained from navigating the Mississippi to that derived from memorizing the Bible. According to Twain, a pilot's memory is about the most valuable thing in the world. On the other hand, knowing the Old and New Testaments by heart, being able to recite any part of them at random forwards or backward, is not nearly as impressive as the remarkable knowledge that a pilot acquires from navigating a river.
What Twain seems to be driving at here is that learning is doing, that deriving knowledge from practical activities is so much more worthwhile than simply cramming one's head with words and trying to memorize them.