If you don't mind "cheating", the easiest way would most likely be using MCEdit or WorldEdit. If this building is massive like you say, it would take a very, very long time to move it above ground using pistons. If you really wanted to do this, though, you would put a piston under a block, activate it with a lever, place a block in the new empty space, and repeat. Unfortunately, since you are supposedly underwater, this would be very difficult.
However, I have done testing, and if you were to push a column of blocks up using a piston and one of them is a water source block, the water simply disappears.
Edit: Now that I see you're an admin on a Minecraft server, I'll give you WorldEdit instructions. To use WorldEdit, first install it on your server. Then use the //wand command to give yourself a Wooden Axe. Use this to left-click on the bottom-leftmost block of your building, and right-click on the top-rightmost block. This encloses your building in a "selection". From there, you can //copy and //paste it wherever you please.
You'll have to make a gate using an assembly table and some lasers. Place the gate on the conductive pipe directly attached to the engine and set its conditional to "Power requested" -> "Output redstone signal". Whenever there is a need for more power on your pipe network, the gate will emit a signal, turning on the engine.
There is a little bit of lag in the engine turning on or off, btw. Nothing dangerous, just something to be aware of.
Best Answer
A pretty good indicator is the color of your engine. It starts out blue and cold, and then progresses through green and yellow to red. Once it goes red, it is a pretty good idea to shut it down so it doesn't explode. If you want to be completely safe, turn it off in the yellow stage, although it can be a bit time-consuming to keep watch and letting it cool down more often.