Hi,
#1: If you don't use the exported code, then the whole meta box settings is saved in the database (under a special custom post type called "meta-box"). The Meta Box Builder will get all the configured meta boxes and pass them to the Meta Box plugin (and extensions).
Technically, meta box settings (an array) is stored as a serialized data in the post content of "meta-box" custom post type.
#2: Yes, definitely. You can use the Export/Import features of the Meta Box Builder to use it on other sites. Or you can just copy the exported code (in the Code Export tab) to use on other sites. Both methods work.