Once I file an application with EFS-Web, do I also have to file subsequent documents with EFS-Web? If I originally filed by paper, can I use EFS-Web to submit follow-on documents?

You may choose to file by paper or with EFS-Web at any time during the application process. The method of filing the initial application does not determine the method for filing any subsequent documents.

USPTO FAQ - Questions and Answers (31AUG2006)