You should think twice before using Thompson's Water Seal. If you are lucky you will get one season out of it. It is a liquid wax based product (not totally unlike the cheap stuff you pay $1 extra for at the car wash) so you cannot finish through it and if it does not wear evenly you end up having to strip it off just like you would a waxed floor. If you can get it out of deck wood grain. It can encourage algae and mold growth and resulting discoloration and staining.
You would be much better of with a penetrating sealer, or a sealer and UV protective clear coat system.
A pump sprayer, sometimes chased by a pad, is the usual recommended method for applying sealers and at least semi-transparent stains. I am not sure you will get the coverage you are seeking through regular spray gear. And again, if you go with Thompson's you will have the wax issue in your spray system.
