Your message is unclear to me.
The website is your hosted website? Or a Filemaker hosting service?
Is the database Filemaker or SQL?
The documents and the links to their location relative or absolute?
Say I want to create a filemaker database and publish it on the web, in order to access it and modify it online. In the database I am going to use container fields that only link to the files. Can I upload the source files in order to open them from the database? I haven't use a web database before, just wanted to know how it works.