Yours are by no means the dumbest questions asked around here and you've clearly tried to find your own answers first so don't sweat it!

I think your problem is occurring because XML::SAX::Writer is receiving multiple start_document and end_document events. When you parse the child documents, you really need to filter these extra events out. You could set a flag in $self before the child parse and clear it after; then add start/end_document handlers which only propagate the events if the flag is clear.