When I dig down, I always dig in a way that I can quickly and easily turn the shaft into a water elevator, so it's a 2x5 spiral staircase all the way down to bedrock (I haven't built a shaft that ran into lava yet). Later, when I change it to an elevator, I simply remove the remaining blocks, pour the water in, and put in a boat.
The problem with a waterway system is that boats tend to break REALLY easily. You have to have all your channels in 7-block increments so that your boat isn't smacking the walls at all.
The problem with a waterway system is that boats tend to break REALLY easily. You have to have all your channels in 7-block increments so that your boat isn't smacking the walls at all.