Individual saves are stored as folders, meaning you never run out of "blocks."
Use the tool mentioned above to import that .psu into your PCSX2 directory.
Nothing is worse than losing 50 hours of JRPG progress. Follow these rules to keep your files "better" and safer:
If you still have your original PS2 hardware, you can bring your childhood memories to the emulator. Use a PS2 with installed.
If you have hundreds of games, one folder or file can get cluttered.