I had a werecapybara in my fort for several years. It's not nearly as hard as people imagine. First, werebeasts only transform on the full moon. (which is every 30 days). Each Dwarf month is 28 days, so essentially, if your dwarf turned on the 28th of this month, then next month it will be the 26th, 24th the next, etc, etc. There is a list of the dates of all the full moons on the wiki.
Dwards stay turned for about 1-2 days. All you need to do is to keep the transformed werebeast out of sight for those 2 days. The easiest way is to put them in the military and station them somewhere. Transformed werebeasts who are stationed will stand there doing nothing *as long as they don't see any other creatures*. They are also building destroyers, so you need to make sure that there are no statues or doors in sight.
The way I did it (which was easy) was to build a hut on the other side of the map. The hut has an opening facing towards to edge of the map (no door!). 1-2 days before the full moon I stationed my dwarf in the hut and then just waited until the dwarf turned back. Then I un-stationed him. You don't need to make a new squad just for your were-beast -- you can station individual dwarfs from the squad menu (I forget the keypress, but it's pretty obvious).
Werebeasts don't need to sleep, but they do need to eat and drink. This means that they might defy your station order to get a drink or food. As long as you give yourself some leeway, it's not a problem, but I always decked out my werebeast with supplies (military supplies menu).
In the even that a disaster happens and your werebeast decides to chase a cat or something crazy like this, the key is to keep him *out of sight*. If one of your dwarfs attacks him, then it will trigger a loyalty cascade. If that happens, you have to close your drawbridge and allow the dwarfs on the outside to duke it out until one side kills the other. *There is no other end for a loyalty cascade -- do NOT try to save them*.
Basically warrens behind draw bridges are your friend. The other main threat is if you get into a siege situation. Station the poor guy on the other side of the defence line and hope he survives until the full moon. You can't afford to allow him to turn in your fortress (I suppose you could wall him up again, though...)
Really, it's quite easy to manage werebeasts as long as you keep an eye on the calendar :-)