I am filing for my LLC. They ask me to put down my physical address. I will not be working out of my home I will do business with non-profit organization. Should I use my business PO Box address as my physical address or should I use my home address as my physical address?
You must use a physical address - NOT a post office box - to identify the primary location of your business. Even if you are doing business with another entity (such as the non-profit organization you reference), your LLC must still have its own business location.
If the zoning regulations for your residence permit a home business, then you can use your residence address for this purpose.