In general, you should know about the exact pinout of the breakout cable or front port and the header on the bord, there basically are only four different pins.
On the cable part, I'm looking at one from DeLock here, the cables are red, white, green, black for vcc, usb, usb, ground. So, every USB header has two of these, the orientation may be the same for both ((USB2 in that manual) or the opposite (USB1 on the same board, for whatever f. reason), but the order of each four most likely always the same and the black wire is ground.
So, that shoud be simple enough.
Btw., "*USB_FP_OC0" on pin 10 is some special MSI proprietary BS, ignore it and don't attach something to it, I'd say.
Unfortunately, much like the status of Ukraine, the world never quite agreed upon a definitive desing for those headers and if the cable doesn't match, it's probably missing a hole which was supposed to keep you from plugging in the wrong way.
Which makes sense as long as you have the appropriate plug for your motherboard, obviously.
IIRC, most are 2x5 with the last one at each end being a second "ground" or unused but anyway, figure it out in the manual an then: Those black plugs are not proprietary and, using a needle or very small screw driver, one can lift the plastic "tongue" from the metal part and then pry out the metal part from the plastic and rearrange them to fit, if nothing else works.
So, if they're missing a hole for your purpose, maybe steal one that does not from somewhere, allowing you to use the actual cables from the front ports.
For the same problem there also are generic breakout cables being sold that use two 1x5 plugs rather than one 2x5, but you'd still need to check what to do with it:
https://www.ebay.de/itm/234187537377?epid=1404130252
So you could flip one of them to fit the header, etc.
A PCI card would have the benefit of providing USB 2.0 and some have internal headers for stuff like front connectors.
Btw., there is an obvious case for the 10 pin "up-down" or flipped arrangement: Those are rotation symmetric, dosn't matter how you attach them. Obvious benefit. Took us only 20 years to figure that out with the USB-C connector.
Alas, the breakout cable I mention above also is of the "mirror symmetric, one hole missing" confession...