I've read through the manual multiple times and I cannot understand what it means.
My MB (ASUS P8Z68-V Pro) has 8 Sata connectors. 4 of them are light blue. Two are cream. Two are dark blue.
The manual says something about the dark blue connectors being 6GB while the bios says the dark blue connectors are 6GB. What does this mean? Do they make any difference if I am just using a standard 500gb HDD? I'm also given 4 cables two of them say 6GB sata on them but they fit in any slot, does it matter which one I connect it too?
Not if you're using the old HDD. But as the manual says, it is safer for you to be using a Standard SATA cable to connect you Standard HDD to the Mobo, you will need to connect them to the Light Blue Connectors on the Mobo.
You ask why?
Well, there, SATA and SATA3.0 standards, one gives upto 3GBps of data transfers and the other gives upto 6GBps of data transfer rates.
So unless you're using a SSD that Dark Blue connector is really not much to worry about.
You need to connect you HDD and ODD to the Light Blue Connectors on the Mobo.