First of all, you need to download the latest ISO Tool provided here:
Once it's done downloading, extract the "ISO Tool 1.XXX" into your desktop and copy the "iso_tool" folder into the GAME folder of your PSP. You also need the untouched ISO in the ISO folder of your memory stick. Once you're done , run the ISO Tool through your PSP.
Choose the ISO you want to patch and press X on it.
Once you've pressed X on the ISO, press X on "EBOOT decrypt" on the "ISO Menu".
For this "Do you want to store a backup of EBOOT.BIN?", press "No". However, it depends on whether you still want the undecrypted/unpatched EBOOT or not, but I usually press "No" since I use 5.00 M33-6 and I don't have a reason to keep it untouched.
For this "Do you want to enable the version patch?", press "Yes".
For this " Do you want to start?", press "Yes".
Once you're done with the EBOOT decryption, press X on "Patch".
Press X on "Patch Prometheus". Once that is done, you're finished. You can now run the ISO you've patched on your PSP.