Hello! The clues at their most basic are just a mechanism to give players something to do in a room outside of encounters, NPC's, traps or if it's empty. Once you collect three clues, then you can roll d20 on the boss weakness table to see what the weakness actually is. The table are just a table, so if your adventure makes more sense to have a specific weakness then go with that.
"Eye Damage" means hitting the boss in the eyes.
"Fire/Ice/Poison" means one of those (player's choice or roll) is the weakness, not all three.
Once you know the weakness, then only by exploiting the weakness do you do 2x damage. So if the weakness is eye damage, you have to during the battle somehow hit the boss in the eyes.
NPC's cannot tell you the boss weakness outright, they can give you a clue though.