Yes it will sound cleaner than the AC'97 BY FAR!!! This circuitry is not affected by the rest of the electronics in the laptop.
Besides - this is a pretty nice card.
Plugging it into the headphone port will also give you nice results. Just mamke sure that you use the Klipsch volume control more than the Audigy volume control. i.e - keep the Audigy volume as low as possible while making sure that the Klipsch volume control is in the mid setting - while making sure you have a volume level that is just one step short of being loud. From here you change volume using the klipsch control and stop touching the audigy
The line in on the audigy is for you to connect SIGNAL LEVEL sources like the output ftom the LINE OUT of a Portable CD PLayer, Digital Audio Player etc.
LINE OUT --> Amplifier --> Speakers
Headphone Out --> Amplifier --> Speakers