What problem exactly are you having connecting those wires? Are you not sure where to connect them or you not sure which wire is positive or negative?
It does not really matter as these connections are for hdd activity lights and power lights and/or switches. You can get either wire to the positive or negative it wont hurt anything. Page 27 of your manual shows you the connector layout.
As for the PSU haivng extra connectors that is fine as you may need more power connectors if and when you choose to upgrade or add extra stuff inside the system. Main connections to be concered about are the 24pin connector and the 4-8 pin cpu connector, you should also have power going to your video card if you are using a add-in GPU. Also your ssd,hdd, and optical drive should have power to them.