So you'd have to shape the bottom of the thing you drop to fit the landing zone to avoid distortions.
Or the top. Or both...
Intention
###
#######
#########
Sea-bottom
\_
##\__ _
#####\__/#
##########
Either or or
### # ########
####### ##### #######
######### ####### ######
####### ######## ####
#### ######### #
Becomes
###
#######
#########
#########
##########
##########
As for clearing the water out, I've heard good things about a ring-platform of (sea-level) floors supporting an array of pumps (perhaps massively wind-powered?). This can (or could, if it's changed) apparently move significant water out of the centre. Making the ring large enough that a second ring can be safely built within this that pumps water at Z-2 out from
its centre, and continuing until you have the desired sea-bed worksite dry (or using a temporary building and re-building to allow you to place 'dam-walls' around the site you want).
I'm a bit hazy about the precise details of the construction process, as I've never tried it myself, but if you start with scaling up the following setup...
~~~~~~~~~~
~++%%%%++~
~++%%%%++~
~%%?%%~
~%%?%%~
~%%?%%~
~%%?%%~
~++%%%%++~
~++%%%%++~
~~~~~~~~~~
...with a larger centre (if you want to
start off ambitious...), then maybe you can figure out the rest...
Ahhh... Catsup has just (better) detailed this method... Darn ninja. @Raphite1: When channelling out, ramps will disappear when all next-door 'solid' tiles are afterwards changed to ramps. If chanelling (or ramping from below, being safer) a 2D block this leaves the odd bit of ramp as an isolated solid block is 'rampified' with no other solid bits adjacent to later be dug out, but if you have a line left, channelling the centre tile (or centre two tiles) and then retreating outwards (or starting at one end and 'retreating' across it) should leave flat floors except for at either end.