The GUI will run the SPROC sp_refreshsubscriptions after adding articles. This SPROC updates the subscription metadata to include the newly added table.

To run this manually, it's a simple matter of including the following in your script:

EXEC sp_refreshsubscriptions @publication = 'PublicationName'

Update PublicationName as appropriate for your publication.

Reference: http://msdn.microsoft.com/en-us/library/ms181680.aspx