I use 1/2 inch galvinised roofing nails the large head hold much better than any t-50 staple. high quality glue is also a good idea, but I use the nails only and they seem to out last the carpet and are easy to remove.
your engine down insures that the lube in the lower unit covers the bearing, gears and seals. In addition the unit up can collect water/condensation and freeze/crack.