PCIe PRSNT# signal connection
PRSNT#1 is hot plug detect and should be connected to the farthest PRSNT#2 pin, so only one PRSNT#2 pin is connected to PRSNT#1. These are connected on your card.

Note that this may not be the farthest location on your physical connector as it gives the host a clue as to the width of the card as PCIe cards are required to operate at their design width (the number of lanes it supports) or the x1 width. 

Even though a card may be a x16 card, it is only required to support x16 and x1 configurations. It is not required to support any other link width (a gotcha that has caught many unwary designers).

A x1 card should connect PRSNT#1 to PRSNT_2(1) on pin 17 (for a standard PCIe slot), x4 to PRSNT#2(2) on pin 31, x8 to PRSNT#2(3) on pin 48 and x16 to PRSNT#2(4) on pin 81.

See this page for details.