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If both HDs have their own systems installed, your Mac can boot off either. The computer's preference for HD/System is stored in the Open Firmware (kinda like a PC BIOS) and is edited through Mac OS X's Startup Disk system preference.
Your Mac should already be set up to prefer its current system, so when you add the new HD and startup, it'll still boot in the existing system. It'll continue to boot in the existing system until you tell it otherwise through the Startup Disk preference.
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