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Sounds like a good idea at first, but utilizing the optibay for your primary OS causes issues with sleeping/waking/hibernating. You can test it out, and see if the placement causes you any issues. It didn't really cause me too many issues, but I was using drive that was already known to cause issues.
This should only cause issues on older machines. If you have 2010 or new, leave the HDD where it is in the factory location, and put the SSD in the optical bay.