Gravity Forms PDF Extended uses Gravity Forms' in built hook to attach the generated PDF to an email. You can use the same hook to attach other files as well, including those uploaded in your form.
You can review the two hooks below:
If you place the hook in your functions.php file and add the user attachments for the form you are after the system will automatically add the PDF from GF PDF Extended and the two attachments you specified.
If you need help with implementation feel free to contact us at enquire[at]blueliquiddesigns[dot]com[dot]au.