first step is to find a good certifier that is not a dick. some of them can be very anal and make life very difficult indeed.
once you get in contact with a good certifier talk through the project with them and let them know exactly what you plant to do and ask them when/what they want to inspect as you go.
if your not sure about the legalities of some aspect ask them.
if you keep them involved with the whole build then certification is easy.
if your in the auckland/hamilton area i recommend getting in touch with Mark Stokes. he's a hard man to get hold of but its worth the effort.