ATmega32U4 instead of Arduino

Hi,

I want to use the integrated ATmega with the Atmel Studio.
The 6Pin-Connector near the Micro USB is for ISP Programming (via PDI, using an external programmer), correct?

You connected two pins directly to two UART-LEDs, is there any way to use the alternative functions of these pins (i.e. the /SS-pin from the hardware-SPI)?

How did you connect the Aref? May I use the internal 2V56 voltage reference?
What about the /HWB-pin? (How can I use it for hardware bootloader activation in your circuit?)

Is there a (maybe simplified) circuit diagram anywhere - ATmega32U4 and your connectors in the U2-area?

Is this substitution correct?
B0 - RxLED (???)
B1 - digital-15 (SCK)
B2 - digital-16 (MOSI)
B3 - digital-14 (MISO)
B4 - digital-8
B5 - digital-9
B6 - digital-10
B7 - digital-11

C6 - digital-5
C7 - digital-13 (LED)

D0 - digital-3 (SCL)
D1 - digital-2 (SDA)
D2 - digital-0 (RXD1)
D3 - digital-1 (TXD1)
D4 - digital-4
D5 - TX-LED (???)
D6 - digital-12
D7 - digital-6

E2 - (???) (/HWB)
E6 - digital-7

F0 - analog-5
F1 - analog-4
F4 - analog-3 (TCK) F4..F7 -> JTAG
F5 - analog-2 (TMS)
F6 - analog-1 (TDO)
F7 - analog-0 (TDI)

Aref - (???)
XTAL1/2 - 16MHz-Crystal?
/Reset - Reset (near digital-5)
USB-Pins - connected with Panda-PC

Thank you

LotadaC