Use a spreadsheet editor (Excel) to define pins for all partitions and then import them in the Symbol Wizzard in Library editor.
Then polish the symbols with symbol editor.
That depends upon the device complexity. My preference is to make a symbol for the programming configuration logic, and then a symbol for each IO bank. That way the power definition for each power bank is defined on the same page as the connections for that bank. With a 640 pin device you may need to break the symbols down farther.