How do I install Yosemite on a 2nd HDD I have added and have the Mac Pro boot from the new HDD?

My MacPro's HD seems to be failing. None of the tests I run indicate that, but I get constant spinning balls and everything takes a long time. I bought a 2nd HDD and installed it in the 2nd bayou my Early 2009 Mac Pro. I formatted it and want to install Yosemite and have the Mac boot off the new drive. It is currently running OS X 10.9.5. When I go to update to Yosemite it begins to download. Will it give me the option of which drive to install on? Or will it just upgrade the original Mac's HD?

A Samsung 850 EVO 128GB SSD $75 now and makes a huge improvement. But get the 250GB which is $99. 500GB $199
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Output from Etrecheck is an easy "quick check" of what your system is carrying around and what baggage it has.
Move data to a 'data and media library" drive.
Use CCC to skip the user data folders except ~/Library and clone to SSD
And might want to save the installer .ESD package for use as clean installer and to be able to boot from.

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