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No worries. OS X is fully SMP enabled, and really benefits from additional CPUs/cores.

OS9 when run natively only used the first CPU. There's a very short list of specific apps that would utilise the second CPU for specific processor intensive jobs - Photoshop v7 being one and also Final Cut Pro IIRC. Classic mode in OS X offloads I/O tasks the 2nd CPU (if available).
 
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