I tried muddying a farm plot by going about it in all the wrong ways; channeling a plot rather than digging one out on the lower floor and then make a hole in the floor above; having a single dwarf trying to muddy it (drying caused a maximum of 3 wet tiles, and it still took an eternity with two dwarves AND rezoning); I also found removing muddy ramps did NOT leave a muddy floor. My experience leaves me to recommend somewhat against wuphonsreach's recommendation, namely to make a slit in the upper floor (if you normally use a 3*3 plot, it would be a 9*1 slit), mark each tile as a separate pond (and yes, it defaults to pit, so the sequence is "pPf" after having defined the zone, using default key bindings). If you're creating the farm upon startup of your fortress, you don't have too many dwarves to manage, so I would micromanage it such that I would remove each pond designation after a dwarf has dumped a bucket of water into it, thus getting rid of the frustration caused by evaporation (and also allowing the job to be done by a single dwarf).
It looks like wuphonsreach is describing a later stage when you want to create a new set of farm plots a fair bit lower down in the fortress; using that method then and there is less efficient than a tile at a time, but it allows you to just start it off and let the dwarves take care of it, and then stop them when the work is done.