Connecting motherboard ?

Question

I took a plan of the motherboard out of the manual . But connecting it is a different story. For instance: Do I have IDE disk 3/4 or 1/2 ? How about Serial ATA 1 o3 2 ? Where do I have to connect USB E/G and or USB F/H ?
So, I cleaned my computer (inside) and disconnected some cable and now 2 USB ports (front panel) do not work any more. I also don't know wether this a software or hardware problem. Before I reinstall my whole operating system I want to make sure that hardware is not the problem and the connections to the motherboard are made properly.