If you're listening to your headphones through your PC, it's better to directly plug your headphone to your soundcard line out than using the headphone socket of a PC speaker system.
Just make sure you adjust the volume (from volume property of your PC) slightly lower first since [soundcard --> headphones] tend to sound louder than [soundcard ---> speakers] or [soundcard ---> speakers ---> headphone]
If it is too troublesome to reach to the back of your PC everytime you wanna switch from speakers to headphone, the method that I always suggest is to get a mini-mini cable extension, plug one end to soundcard out, and the other end to your speaker line cable (that leads to line in of your speaker system).
Make sure the connection between the mini-mini and the speaker line cable is around in the middle of your monitor or somewhere you think is handy so it's easy to plug and unplug it. that way when you wanna listen to your headphone, you won't need to reach to the back of your PC anymore, since the connection is near you, you can just reach in and swap.
Not sure about the headphone out from your 5500 speakers, but from my PC speakers, the difference between listening to A900 from speaker's headphone out and from direct soundcard is HUGE.