Filemaker can 'store' the document both ways, but by many orders or magnitude I recommend storing by reference.
Stop Embedding Documents in Your Database!
Recently, I converted two customer databases from FileMaker 11 to FileMaker 12. Both customers were embedding documents in the database by inserting them into container fields. The result in each case was database bloat—a file size much larger than necessary (1GB or greater).
The disadvantages of a large database in FileMaker are several including slower performance (more data to push over network), lower productivity (long wait times during backups), and greater risk (more susceptible to corruption in the event of a crash). Fortunately, FileMaker 12 has a new feature called Enhanced (or external) Container Fields to address this.