The way I do it once I am satisfied with the final mix;
Line out soundcard to external mixer
From external mixer to Line in soundard and record as pcm stereo wave file if I need sounds from my soundcard.
As I don't have a dat recorder I have to use the analoge line in, so usually there's some
(allthough not much) noise from the analoge line in of the soundcard, which I denoise with cooledit.
Lately I much more use multitrack software and only use external gear also the midi is coming from my keyboard which overall has much better sounds as the soundcard banks..
Keyboards/Sound Units: Kurzweil 2600S, Roland VR-760, Acces Virus C, Roland G-800, Akai AX60, Minimoog, Machine Drum, Roland R8-M, mediastation x-76