The motherboard that I'm going to buy is the MSI FM2-A75MA-E35 Micro ATX Board and is displays that it has USB 3 onboard so I can use the USB 3 on my case. But there is a problem, the USB 3 Cable on my case has a USB "end" in the other side instead of a pin plug in...thingy. I'm using a MSI TC- 128 case (I know it's bad but it works). Is there suppoused to be some sort of adapter I'm suppoused to get or...what?
It's a pass-through cable. You route that cable to the back of the case and plug into your motherboard's USB 3 ports at the rear I/O.
I'm not aware of any adapter that turns a USB to a USB header.
I believe what you're referring to is is simply a USB connection that you'll have to route through the back side of your computer chassis, through a grommet and outside of the computer chassis and connect it to the back side of the computers motherboard, essentially creating a connection from the cases 3.0 port to the MB's 3.0 port.
This was common on the first generation cases using 3.0 connections on the case itself since many first generation USB 3.0 boards didn't have pin headers for some reason.