Of course you can put files on it.
And yes you can put Windows on it.
Now here is the kicker you cannot install Windows from an external USB optical drive or flash drive on a Mac. This is an Apple limitation for any Mac with a built-in SuperDrive.
If you want to install Windows:
Don't try to use BootCamp Assistant; that will simply tell you to format the entire drive for Windows (unless that's your intention)~
Instead simply go to Disk Utility, and go to the partition tab. Click the little plus and add a partition. Give it a name you'll remember, but don't waste your time on it (reason comes later), so don't spend forever thinking up a name or picking the format; just pick Mac Extended; pick how much you want partitioned to Windows and click Okay. It will partition out this much space.
Now you need to move your optibay into the main bay and reinstall the SuperDrive. Boot up while holding the option key. Then choose the Windows installer. When it asks for the place to install, pick the partition your sized up earlier and click format; this will format it and give it a default name (why you shouldn't bother with thinking up a fancy name earlier). After everything is done, you can remove the optical drive again with your optibay HDD back into the optibay and whatever drive you had back into the HDD bay. You don't need the internal optical drive for anything, but installing Windows for the first time (and subsequent reinstalls); if you need to install software or playback a movie, an external drive will work fine.
Since you can't use BootCamp Assistant to install, you cannot default the boot to Windows via the Startup Disk prefpane, you need to either hold option every time you boot to run Windows or install rEFIt which gives you the option every time you boot.
(In case something has a Mac without an optical drive [ie: MacBook Air or MacBook Pro with Retina display] Apple lets you install with an external optical or USB flash drive)