You may refer to the user guide:
https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/ug/ug_dev_specific_pdn_20.pdf
and also a training course....although it mentioned it is for Stratix3 and Stratix4, don't worry about it. The concept is the same.
https://www.intel.com/content/www/us/en/programmable/support/training/course/opdn1100.html
After watching the above training course, you will find that ... overall, all you need is to feed the spreadsheet some info to find out what is your Ztarget and board info for the Feffective. Then, once you have that, it will populate a list of capacitor that can effectively reduce the impedance on your rail.