Question

What is the proper way to quote something quoted in the bible? Here is the exact quote from the bible...“Why were you searching for me?” he asked. “Didn’t you know I had to be in my Father’s house?” The words...he asked...are part of the quote.

Answer 1

You change the quotations to a single quotation and put quotations on the outside.. Instead of having it say : "Why were you searching for me?” he asked. “Didn’t you know I had to be in my Father’s house?”, you write:
" 'Why were you searching for me?' he asked. 'Didn’t you know I had to be in my Father’s house?' ”

Do you get it now?

Answer 2

also after the quote you should put the bible verse...(ie) John 3:16

Answer 3

To be perfectly correct, you cite the verse and the version of the Bible it appears in.

It also depends on what Style you are using. If you have a required style, let us know.
If not, here is the MLA format:

(It is at the bottom, last category - Other Print/Book Sources, first option)
http://owl.english.purdue.edu/owl/resource/747/06/