Please understand that not all of the powersupply wires need to be connected. Some of them is just left there so you can add more parts to the system if you wish in the future.
But you have to make sure the important parts is connected. Check the parts.
1. All the hard drives will need the sata cable connected to the motherboard and a power cable from the power supply
2. A power cable is connected to the motherboard.
3. Any additional connection for your PCI cards. Like videocards/wireless cards. But please know that not all cards require power connector unless required.

If you mean no problem is comming up then is fine. Extra cable is in every system. But you can check for overheating and all the info of the desktop by Everest if you want.
http://www.softpedia.com/get/System/System-Info/Everest-Home-Edition.shtml

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