well I am not sure if it would confuse him. The thing is does he actually have to go that much or is it just because you are trying to housebreak him that you do it so much. If he can hold for a bit longer then I would take him. While I am home I think Lex can go two hours or maybe more without having to go outside. It also helps that I don't leave his water down all day either.
I would love a job like yours. Your boss sounds great. I bring my little guy to work once in a blue to visit with my boss. I would love to bring him to work with me every day. It sure can save on a baby sitter hassle.