It'll be fine, USB 3.0 devices will work fine in USB 2.0 ports. If you try to install Windows via a USB 3.0 port on your computer, it probably won't work as USB 3.0 ports require drivers and some boards can't use them for boot up.
Short answer: You can use the 3.0 drive in a 2.0 port. Do that, install, be happy.
Thanks for the help!