Gumpness aloud my friend 
Setting the clock in your soundcard to the 6Q(spdif) is a global setting in a sense. You should definetly be able to use your soundcard just as you did before, only difference being, that it will clock from the 6Q rather than internally in your soundcard. They should co-exist with no problems.
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Pentium Processor Ex edition, Sonar 7.0.1PE and 5.2PE, Motu 2408mk3, Apogee Mini DAC, Motu Microlite, 2x UAD-1, Presonus Digimax FS, Big Knob, Joe Meek 6Q, Toft ATC-2, MPA Gold, Vintech Dual72, Line6, m-Audio, etc etc
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