If you can get a panel header from a generic AC97 panel and cut off the leads on your wires and had a wiring diagram to wire it up... then you could use both. It's a lot of work if you can't find the wiring diagram or aren't experienced with wire stripping and soldering.
Another option is to plug it into the rear as I suggested and then plug you speakers into the front, and when you want headphones just unplug the speakers from the front and switch.
I don't know exactly how your case is wired, but the AC97 panel header should look like this...
So it is just a matter of cutting the wires, stripping them and knowing which one should go where so you can stuff it into an AC97 header or splice the wires together, solder and tape them off.
But the easiest would be to plug those jacks to the back of the board and use the front for your speakers and headphones... just switch them out as needed.