From my own two experiences being on the receiving side of polygraph prescreening, I do not think the polygraph should be used at all during the fact gathering process.  The NAS report strongly states that no employment decision, either POSITIVE or NEGATIVE, should be based on pre-screening by itself.  Yet in most Federal pre-screening  uses, it can stop an application in its tracks without any further investigation.  This is WRONG!  As people find out that polygraphs used in this way do not work, they will not confess anything, and the whole polygraph process becomes a moot point.  

If I agrue with someone that they owe me twenty dollars and they say they only owe me ten,  I would suggest to take the ten dollars that we agree on and keep negotiating the rest.

The NAS was rather specific to pre-screening and screening polygraphs about the fact that they find them ineffective to predict if someone is a threat to security (the whole of a background check).  Let's take this off the table and then we can possible discuss other polygraph procedures which need further investigation.

If there are other legitimate uses of polygraphs (subject to great debate on this website), further research will bear this out.  The pre-screening and screening issues will constantly cloud the discussion and must be taken off the table of discussion by their removal from use by the polygraph proponents.