You will be able to fight the Golden Poo Snake once you obtain the Mechat on disc 3.
You will need 2 items to fight him: without them he will just run away everytime.
1. Shoes of Hermes: Found behind a Black Barrier in the ground floor of the Ancient Factory. The Black Device is obtained after defeating the Sea Dragon at the bottom of the Sea Cube. This item will give you first strike in battle every time.
2. Poo Bracelet: Found at the Gate of Jibral Castle in a blue chest. The blue device is obtained through normal story progression. The Poo Bracelet will kill the Golden Poo in one hit, as well as any other Poo monster (besides King Poo).
After obtaining these 2 items you will be able to take out the Golden Poo, equip both accessories on whoever you want.
He is found on the Southern Deserted Island at the far south of the map (it has a little plateau in the middle of it) here the only monster that will appear are Golden Poo's.
Check the video below for a visual location.
This is a great area to get the 1 Million Gold achievement as well as leveling your characters to Level 99.