9V is 9V and G is G - Just connect whichever 9V is closest to your power supply jack.
For instance, if you wired the topmost 9V pad to your power supply jack at the top of the enclosure, you could use the bottom one as the 9V supply for your indicator LED (via a current limiting resistor). That bottom ground pad could be used for similar purposes.
OK now having looked over your picture a little better, you can just use those two pads unconnected, just ensure those bottom ones are connected to the appropriate places. The G needs to go to ground, which will be your enclosure - in most instances it will ground to this via the sleeve of your input jack - you can check this connection by getting your multimeter and checking for continuity between the enclosure and the sleeve. The 9V pad should go to your 9V jack
