The first question is slightly unclear, but, here goes,
The front panel connectors on your case should already have the plastic rectangular sort of pin socket connectors on them which plug into the Mobo. The mobo must have internal USB/firewire etc etc sockets on it.
The same sort of connector is there for the Audio and you need to plug that into the Mobo header provided, you have it on the board.
No, it will not switch off the rear audio panel unless and until you plug something into the front panel.