Oh yeah! I remember this. In "Chocolate with Nuts", Patrick reads the sign that says "Eat Barnacle Chips. They're delicious" and Spongebob responds back by saying "They are most certainly not delicious". Patrick then says "Not the way I use 'em."
Hmm...I wonder about this. Probably for combining them with foods that are bad matches to eat both with. Since Spongebob criticises the chips about their taste, Patrick maybe said "Not the way I use 'em" to reference about the foods he eat with the chips that are good to him but not with everyone else. I hope that this doesn't sound too confusing, but this may be convincing.