Newbie: ATmega32u2 USB-powered application - which variant?
Use whichever suits your application best (what voltage I/Os do you need?)  

I imagine there is an internal 3.3V regulator which takes the 5V VBUS from the USB and regulates to 3.3V, which is then output from UCAP pin and can be used to supply the VCC for 3.3V operation.
For 5V operation the VCC is simply taken directly from the 5V USB VBUS.