Jim Kennedy referred you to the right section - it's complex, but not that bad - that explains how hole handicapping is supposed to be done.
One thing to remember is that hole handicapping is NOT done by the course raters, local association, or USGA. Each club does that themselves - and they can and probably should follow those USGA guidelines - but they certainly don't have to.
Jim F, in your case, I'd be kinda reticent to lower the stroke allocation too much for a long par three. Yes it is a very tough hole relative to par, without a doubt. But the key concept as several have stated already is "where does the higher capper most need the strokes?" And a long par three usually means the high capper makes a 4, the low capper does also... so the stroke isn't needed as much. The other key concept is that the longer the hole, the more shots the higher capper has to hit, the more he screws up and the more distance he loses to the lower capper... so he needs the shots more on longer holes.
Of course specifics of a given hole can change things - like 16 Cypress with the ocean in play - but in general, long par 3s, even being as tough as they are for the low capper - don't get the low handicap stroke allocations numbers.
TH