use of 'in which'

Hi,

Whenever I see the types of phrases like 'in which' in sentences and not so sure of their correct uses, I go back and reconstruct the sentences to get a feel of what they might look alike when made into my version of parts like this:

There is a box in which you can find some stuff you can use.

Here, it is clear that 'in which' is correct because any way you make it, its 'in', not 'on' or others.

You can find some stuff you can use in the box over there.

But for some sentences, it is not clear.

The reference in which the word appears is ...

Here, I am not sure whether should use 'in which' or 'on which' but I probably will go for 'in which' because 'reference' should be a book or source of knowledge in tangible form (most likely), and one would look through a tangible reference source.

So, deconstructing to see if they make sense is the only viable approach for someone who has this type of dilemma?