Because of its plain text underpinnings, and that Pathagoras doesn't convert text in and out of Word as some programs do, Pathagoras is compatible with any numbering scheme you have adopted. However, Microsoft's rules and requirements to insure that numbering schemes between different documents being assembled must be adhered to. They are discussed below.
Also discussed below is a plain text approach to APN. Just insert the characters '#. ' where you want a new number and Pathagoras will oblige.