If the assembly is 'ordinary', it's a matter of grinding away the zinc from the area to be welded. The zinc produces fumes as well as causing 'spattering'.
Once the weld has been completed and the flux/slag removed (assuming stick), wirebrush the surface and apply a coat of inorganic zinc rich primer. For greater protection, a coat of aluminum polyurethane and a suitable topcoat.
If greater cleaning is required, you might consider a portable sandblaster with 'low dust' grit.
If a more specialized means of protection is required then the system goes up from here. What is the reason for the galvanized piping in the first place?