Little endian refers to a storage of values beyond one byte. It's also known as LSB (least significant byte), since the low byte is stored first leading up to the high byte. It's a contrast to big endian which stores in the opposite fasion. The SNES CPU (65c816) uses little endian.
The 16-bit value $5035 would be stored as $35 $50 in ROM and the 24-bit value $708000 would be stored as $00 $80 $70. Note how the high byte comes after the low byte(s), and the bank byte after the high byte. That's how little endian works.
The parameters of the opcodes are stored as little endian too (ONLY if they're numbers), but the opcode themselves are not. For example, LDA $449922 would be stored as $AF $22 $99 $44 in the ROM. The first byte is the opcode; it doesn't participate in the little endian concept. Therefore, it will remain as the first byte to appear. Its parameter, $449922, does participate though.