Actually there are some awesome tricks I used to build Atlantis on my server--they all stem from the fact that water cannot occupy the same square as anything else.
First of all bring a door with you. When you are down there, set it on the ground, open it and step in. You will be in an air bubble. This can be done any time to catch your breath and it's not a bad way to escape from monsters at night.
Secondly signs, ladders, fence-posts all resist water and can be used as blockers. I played with all these for a while:
Signs aren't stackable, you spend all day running back and forth building them.
Fence-posts block you so you can't just swim up and down, overall they will work but are unwieldy.
The best solution I found was ladders--but place them ABOVE your head. You can still jump up and down through them, but if they are at your level you will climb up them every time you move--it's really frustrating (This is no longer true in the latest version making ladders the clear winner).
There is a pattern where you have one block above you with ladders on each side, the a "Knights move" to the next block with ladders on each side. It makes a good roof with no more blocks than you need.
If you want the water to be right over your head in some areas, use signs.
The knights move I was referring to is the L shaped move they make in chess. You can make a ceiling of blocks like this:
. . . . * . . . .
. * . . . . * . .
. . . * . . . . *
* . . . . * . . .
. . * . . . . * .
. . . . * . . . .
Where the "*" are blocks and the "." are empty space. Note that in this pattern, each "." is adjacent to a * (and therefore are actually filled with a ladder attached to the *).
Best Answer
There are several mods that introduce items that speed up the tick rate locally. Examples include time torches and items similar to them. Now you want to put this next to the Smeltery controller.
Between Ender IO, AE2, and some nifty redstone, it can be fully automated.