I didn't understand how MOSS 2007 knows, to what repository an official file should be send. Well it is based on record routing ('doh). BUT, the 'Title' of the record routing rule MUST be the same as the content type name... This is here and pretty confusing, to me at last.
Also, a document will be send to only one document library in the record repository. You can add more routing records that match the same content type. You will get no warning or error but the document will be handled by the FIRST routing record.
More info about it can be read here