you can store the documents in the mysql database. create a blob field in a table and when they upload the file, you can do something like this:
$file = file_get_contents($_FILES['file']['tmp_name'];
$file = addslashes($file);
mysql_query("INSERT INTO files VALUES('username', '$file');
also, if you arent familiar with file uploads
in the $_FILES['file'] part, ['file'] refers to the name of the field in your form.
be sure to stripslashes when you pull the doc file out of the database as well.