I am not sure I fully understand your problem.
Normally front audio and USB connectors from the case look like this.
Are you saying that yours are different? That the front audio is separated in to line in and headphones?
What case have you and more importantly what motherboard have you? I assume that you have had the front audio connected to the motherboard prior to getting the sound card? If so how did you manage this if the cables are separate?
Again I am confused by the USB problem so really do need to know what motherboard you have so I can look at the spec.