I am not sure I understand your question, but in case it's what I think you're asking...
You will need the root path as well as the file name you use to store the file to create a proper database entry. You have to use a mysql databse and and an insert query to input it as long as a select query to retrieve its location and use it in your website.
Read the basics of PHP/mySQL at w3schools and also considering FPDF, read the uploaded FAQ here.
