There's a Notes API that allows you to access Domino servers, databases, views and documents.
There are two JAR files you can use. Notes.jar allows you to access a Domino server locally (i.e. the servlet must be on the same machine as Domino). NCSO.jar allows you to access a remote Notes server from Java. Search Google for Notes.jar and/or NCSO.jar; there are plenty of examples.
Using this API you can add documents to databases.