J.D.
My husband works from home too. He is here all day. We have a closed door policy. If his office door is closed, my 2 year old knows Daddy is working. She is not allowed in his office unless he leaves the door open. If she throws a fit, she gets time out. This has worked and she knows when we tell her Daddy is working she does not disturb him. You have to be really strict with work time and not waver or it confuses them.
Also, I do not restrict my husband's work schedule. He has to work when he has to work. I do not expect him to be out of the office at a certain time. That is his job and he works hard to allow me to be home with my daughter. There are times work has to come first. It is not all the time, but it is one less stress on him if I'm not pushing time constraint. He does take time during the day for lunch and afternoon snacks so my DD gets her time with him too.
GL!