Jeff,
It is a good idea to seal the end grain both when you get the timbers and after the joinery is cut. Don't forget the end grain in the mortises. I use Landark soft wax (I don't have the contact info with me in the hotel) to seal end grain, as I find that it doesn't stain the timbers as much when you slip with the brush. A cheaper alternative is anchor seal or any log sealer. One gallon should be enough.
Good Luck
Gabel Holder
