Few points of correction:
- Schematic:
--- It's best to put a no-connect on all unused pins
--- Connect VBUS to VCC
--- Leave the AREF pin floating (No-connect)
--- A 1uF capacitor close to the USB port is highly recommended
--- 4 0.1uF capacitors between the VCC/AVCC and GND pairs is highly recommended. The four pairs are 14-15, 34-35, 44-43, 23-24.
--- Pull the rest pin high via a 100kOhm resistor
--- Have a debug LED (Preferably on PD6 as it's the one used on the Teensy as well). This can be very handy at times.
- PCB:
--- It's best to not have any traces under the crystal, on the layer it is mounted as well as all other layers underneath.
--- The 4 0.1uF capacitorsshould be placed as close to the atmega as possible.
--- Why the the extra space up top, it's entirely possible to have the components in between the switches, just have to get a bit creative, unless of course if your designs asks for it, then it's all cool.
The atmega32U4 ships with Atmel's DFU bootloader. No need to flash any other bootloader, it works fine via FLIP or dfu-programmer.
From the components you have, the MCY would be the hardest to solder, but that too is not too hard, as the pins are spaced out comfortably. See some YouTube videos on soldering QFP packages, just use solder sparingly and flux liberally.