Use Clone CD for ALL of your PS2 cd based games.
Use Primo DVD or RecordNow Max for the dvd based games. You can find tutorials for these two programs at the top of the PS2 forum in the "stickys"..
You can find how to boot your PS2 backups using the Neo Key at the top of the PS2 forum in a "sticky" that I posted....(boot procedures for all mod chips)