If your save is not a .ps2 file, you need mymc (download via GitHub or PCSX2 tools).

Each character has two selectable Jutsu. For example, Kakashi has his standard Raikiri and the Mangekyo Sharingan. These are grindy to unlock. A 100% file gives you every alternate Jutsu, allowing you to experiment with the most powerful cinematic ultimate attacks on day one.

If you find a save file in a format like .max (Action Replay Max) or .cbs (CodeBreaker), you cannot simply paste them into the folder. You must convert them.

A common point of confusion for new emulator users is the difference between these two.

Recommendation: Use both. Use the Memory Card for your main progress and use Save States (usually F1 to save, F3 to load) to retry difficult battles instantly.