If you want to put the config together with the .ISO.BIN.ENC, the names should be:
/dev_hdd0/PS2ISO/Naruto Shippuden - Ultimate [SLES_556.05].ISO.BIN.ENC
/dev_hdd0/PS2ISO/Naruto Shippuden - Ultimate [SLES_556.05].ISO.BIN.ENC.CONFIG
or
/dev_hdd0/PS2ISO/Naruto Shippuden - Ultimate [SLES_556.05].ISO.BIN.ENC
/dev_hdd0/PS2ISO/Naruto Shippuden - Ultimate [SLES_556.05].CONFIG
You can add the CONFIG file in the PS2CONFIG repository like this:
/dev_hdd0/game/PS2CONFIG/USRDIR/CONFIG/ENC/SLES_556.05.ENC
You only need to include the title id in the file name like you did:
/dev_hdd0/PS2ISO/Naruto Shippuden - Ultimate [SLES_556.05].ISO.BIN.ENC
Other formats supported for the title id in the file name are: [SLES-55605], [SLES55605], (SLES_556.05), (SLES-55606), (SLES55606)
In the PS2CONFIG repository only SLES_556.05.ENC is supported.