It sounds like you two are already doing well trying to figure it out together! As a nanny, if the 2 yr old starts crying, I would prefer you stay in your office and let me sort the situation out.
What helps a lot with my previous families is if you can establish some set times during the day where you can pop in and interact with the children for a bit (maybe everyone has lunch together or you read a short story before nap). That way the child knows when to expect a bit of mommy time, and if the 2 yr old has a difficult time the nanny can reassure them that they'll see mommy for X activity.

I put a hanging sign on my door - one side is green and one is red. If it's green they can come in and play quietly and if it's red they can't come in.

Hello, I've just transitioned into a teleworking position after a period of extended (>1 year) leave. I am in our house (not huge...around 2000 sqft) most of the day when I am not traveling. I just hired a new nanny to be at home with my 2 yo and my 5 yo when he gets done with PreK. Nanny is excellent--helpful, easy going, self-directed and positive...but this is a new situation for both of us and I am trying to figure out how to support her as she transitions into our family, while staying out of her way while she establishes independent routines. For example, when the 2yo starts crying abruptly for mom, is it best for me to stay hidden in the office, or does it look like I am avoiding helping with my own child?

She and I are talking about it (she has never been a nanny for a WAHM) and we are trying to figure it out together, but I would love some insight as to how people have made this arrangement successful.

Thanks!