You're referring to 8-pin EPS plugs right? (Check the keys for pin here
to confirm) There's hardly any server motherboards needing two except extreme enthusiast boards e.g. eVGA W555
or the upcoming MSI XPower X58 Big Bang.
Plugging into PCIe on a modular PSU will not work. 8-pin PCIe
has three 12V+ and 5 ground wires instead. Also the keys on pin are different.
Your best choice is to use a 2x molex->EPS adaptor to gain the 2nd 8-pin EPS plug.