“'I’ve tried going through My Computer, finding the device, and disconnecting it there. But I’m not sure that works…”
What doesn’t work about that? Do you see the device in my computer at all? Can you explore the device, and things of that nature? What if you switch modes on the device, by going through the settings>usb mode options.
personaly, I rarely disconnect and run into issues because of it (unless its downloading or something like that).
In auto-detect / mtp mode you can just unplug it. You should have the option to (if you want) to safely remove the device in the bottom right of the system tray, where the time is.