I use an iMac myself.
I Definitely have a different setup than you: One that is in the iMac itself (which I'm currently using). and another OS that I installed in an External HD. They both have the very same OS installed, but the External one is in case anything should happen to the Internal one. I use the External HD every other week.
I have a Second HD in use for videos and pictures, files and so forth. I don't use the Internal drive for anything except Temporary files.
BTW: Several years ago I installed the OS in a Flashdrive. It worked too! The problem was that a USB 2.0 Thumb Drive is good for Offline usage only: Data Transfer rates were too slow to practically use the Net. With the prices with Plug-and-Play HD's it would be interesting to install the OS in of of them, reboot to the PaP, revert when finished.