Basic furigana means, for 絶対{ぜったい}, 'zettai' is how you read 絶対...period.
For the non-standard cases, think of it basically the same way, but with a little twist: for 巨{おお}きく, 'oo' is how I want you to read 巨.
As a deeper example...
泥棒{おまえ}は信用{しんよう}出来{でき}ない。
If this is a line of dialogue, the person is saying "I can't trust you", but the implication is that "you" are a thief, and that is why you cannot be trusted.
When the furigana are not standard, in my experience, the furigana is what is said, and the kanji is what is meant. For your example, there's not a lot of difference between 巨 and おお(きい), but it should be basically the same thing: おお is how it's said, but 巨 is the underlying meaning.