which is right?

Ex) Make a Luck (-5) [2] check, his Luck value is 3

the modifier is -5, the difficulty is 2.

1) first spending 3 clue token, roll a dice, the result = 5, one success

then spend 1 clue token, roll a dice, the result =6, one success

this check pass.

2) first spending 1 clue token, roll a dice, the result = 5, one success

then spend 1 clue token, roll a dice, the result =6, one success

this check pass

The latter. No matter how far below 0 a modifier takes you, a Clue token always gets you a die.