Here's my method (illustration below, farm in progress): I dig an 8x8 room and channel out the interior 6x6 square with some stairs down for access. Once you've got that, you need to designate pond zones on the upper level. Only one dwarf will fill each pond zone at a time, so I like to designate six 2x3 pond zones.
Pond zones: i brings up the zone menu. Hit enter to start drawing a rectangle, then enter to set the other corner of the rectangle. Now you have a generic zone that's flashing. Press p (lower-case p) to make it a pond/pit. Press P (capital P) to change the zone settings. Press f to set the zone as a pond. Press esc to go back to the zone screen and draw your next zone!
Now you need free dwarves and plenty of buckets; they don't use buckets very efficiently. If your dwarves act too slowly, the water will start to evaporate, but I find 6 ponds with 6 dwarves will fairly quickly fill the farm area. If you have a stubborn spot that just won't fill, move your zones around to target that spot. If the stubborn spot is in the middle, well, be patient. :)
Once you've got mud on every tile (look, k, should show you mud) deactivate and/or remove your pond zones (via the zone menu) and then build your farm (b, p)! Don't forget you can size your farm plot with the umkh keys.
Advanced tip: I like to create a furniture stockpile that only accepts buckets near the water source to decrease the time dwarves spend running around carrying buckets.