I know I can just upload the file to a folder in my server, save the directory location to the MYSQL database, and create a download link based on that directory location but what happens when you store a file like a pdf or zip archive directly on the MYSQL database? How do you retrieve that data and create a file download link then?
You will have to set some content headers before outputting the data from your database, like:
header("Content-type: $type");
header("Content-length: $size");
header("Content-Disposition: attachment; filename=$name");
header("Content-Description: PHP Generated Data");
echo $data;
Full example at http://onlamp.com/pub/a/php/2000/09/15/php_mysql.html?page=3
You can create a php file like "download.php" that put the headers of that file type (and size) and the echo the contents of the file stored.
You shouldn't store file data in your database, that's what the file system is for!
However to answer your question you would store the file contents in a BLOB field which contains the binary data, then to download throw the correct headers and echo the field value.