I was told when I got my tractor that you should keep a layer of grease on the outside of the PTO shaft down near the seal.. under the cover.. to prevent the outside of the seal from drying out. It also is a good idea to run the thing every few weeks for a few minutes just to make sure it's limbered up. It shouldn't have to "seat".. or wear in though.
Same advice from the dealer about the hydraulic seals on the 3pt, loader, backhoe.. any implements.. they can dry out if they are not coated with grease on the outside. I actually had a seal on a loader cylinder develop a leak where the lip of the seal had curled out during a cylinder extension after about three weeks of no-use.