well, with an aquifer in the way, you pretty much need to use a method to breach it.
There are plenty of methods for that (one mentioned here already, and others), but one of the faster (and more dangerous)methods is to dig out the aquifer layer cave in ground from a higher level the dropped earth will be safe to dig through. Without stone for gears, there's no completely safe way to do this, but who needs safe, right? (it's a bit more tricky to do when you have a 2 level deep aquifer, but you can plan for that.)
for desalination, pumps don't need gears to be used, and you can even make a powered pump (that's always on) with a little planning by using axles and pumps instead of gears- just make sure you have everything constructed before you build the connection to any power source, or you may experience !!Science!!
██████████ Z = 0
|||.██+++█
.%%=%%+++█
++████+++█
+++++█+++█
█████
██████████ Z = -1
++++██████
+██+██████
██████████
Assume everything here is constructed and there's a water source off to the left feeding the pump and wheel.
Theoretically, once you start cranking the west pump (both set to pump west to east), it should create flow to turn the water wheelto power the pump, which will transfer power east to the next pump through the axle that connects them, which should allow that pump to move the water that drops and pump it in to the constructed cistern.
One thing I noticed in an older fort (playing the 2010 version of DF)was that water pumped to a Z-level below sea level may not desalinate, and that water behaves funny moving up or down at sea level