WARNING : This is a newbie question.

I am currently trying the demo version of Bookends + Scriverner. I am delighted with the functionality and seamless integration between the two, however I have some difficulties in trying to scan the document, to ensure that the right formatting appear in my intended output (either PDF, or word document).
Long story short, I am looking for simple guideline on how to use Bookends + scriverner, from the dragging of reference in BE to Scriverner, then what needs to happen ?
As I warned you previously, this is a newbie question.....but I am stuck on this for a while now, and couldnt get any instruction from any web on the net.
Thanks.