I was confused about this myself but I think you can tell when its marking if he is peeing just for the sake of peeing. That is to say, if you have already taken him outside to do his business and yet he still lifts his leg in the house I'd say he's marking. Also, the marking is almost always a smaller amount of urine than an actual potty run. I find that whenever I take Nikko outside he will lift his leg at every pole and post so as to leave his mark for the neighborhood dogs.
Sometimes he even runs out of pee and he still lifts his leg anyhow and tries to squeeze out every last drop.
