I have two sources of power inputs.
One of the source is a '5V' from PCI and the second source is also a '5V' through a regulator, on the board. The second source is through a jumper selection.
Question is: how safe is to drive a single supply through two different sources, on a board?
All you have to take care of is to isolate the two supplies. Else the lower voltage supply will be driven by the higher one. You can make the ground common, and add some circuit (or even a simple schottkey - low drop diode) to switch between the two supplies.