Your link above is to iTunes rather than to the App Store. Can you confirm that you are using the App Store rather than iTunes?
"Install OS X Yosemite.app" is downloaded to your Applications folder, not to your Downloads folder. If you already downloaded it to install on your iMac, and didn't take steps to make a copy of the installer before running it, then the installer is gone, because it deletes itself after it completes the installation. It should still be possible to download it again, however, from the Purchases section in the App Store.
You don't want or need to install an OS on the flash drive in order to install Yosemite on a different computer: you want to a bootable installer on the flash drive. You can use DiskmakerX to create a bootable installer on a USB flash drive. http://diskmakerx.com/.
BTW it doesn't matter if your computer boots from another drive on which you have just installed an OS. It's normal, and finishes the installation process. You can switch boot drives anytime you want using Startup Disk in System Preferences.