In manual for ATmega32u2, there are two slightly different diagrams for powering the µC via USB. One of them is described as: "with 3.3V I/O", other: "with 5V I/O" (see images below).
For 3.3V, VCC and AVCC are connected (together with UCAP) to decoupling capacitor, while for 5V, they're connected (together with UVCC) to USB's VBUS power line.
Why? How can I decide which configuration to use?