1. First of all, you need to download ISO Tool 1.65 and extract it. Download ISO Tool 1.65 here.
2. Copy the iso_tool directory to your ms0:/PSP/GAME/ directory. You can either copy the files directly to your memory stick using a card reader, or put your PSP into USB mode and copy the files to the drive letter that appears.
3. The ISO Tool 1.65 should show up in your Games list in your Memory Stick. Find ISO Tool 1.65 and run it (press X).
4. A simple text-based GUI appears, which is actually much easier to use than Eboot Exchange, in my opinion. There are two sub-steps: First you must decrypt the Eboot and then patch it to the file.
5.Use the D-pad to select the game you want to decrypt and press X.
A submenu comes up asking you if you want to make a backup, but select "no".
Another submenu comes up if you want to make a backup. Select Yes.
Finally another submenu asks you if you want to start. Select Yes.
6. Once the Eboot has been decrypted, you must now patch the ISO (Remember that CSOs won't work).
Navigate to the ISO file that you just decrypted and press X.
On the submenu select "Patch"
On the next submenu select "Prometheus method".
7. Your ISO file is then patched with the newly decrypted Eboot and is ready to run on M33 5.50 and Gen-Dx custom firmwares!
If you are running M33 5.0, then you really should upgrade to 5.5, but if you absolutely won't upgrade, then you have a few more steps before your ISO file will work...
8. Navigate to your ISO and press X.
Choose PRX Import
Now your game backup will work with M33 5.0.