Adding your own data in the GdaMetaStore associated to a connection is a possibility to avoid for example to have another file to store your program-specific data (which you obviously don't want to store in a connection).
Doing so is as easy as getting a pointer to the internal connection used by the GdaMetaStore associated the connection, and then use that connection directly as any other connection object.
However Libgda has some specific API to make this easier, described in the section about adding custom data to a GdaMetaStore.