Looking at the datasheets for the AVR64DA28 and AVR64DB28 there are a few minorish differences for capacitors.

For the AVR64DA28 for the main VCC pin decoupling:

100 nF capacitor for the main decoupling

a 1-10 nF capacitor for decoupling at HF frequencies

a 1 uF capacitor listed as optional

For the reset pin:

100  nF capacitor

For the AVCC pin decoupling:

nothing listed

For the AVR64DB28 for the main VCC pin decoupling:

1 uf Capacitor for the main decoupling

10-100 nf Capacitor  for decoupling at HF frequencies

For the reset pin:

1 uF capacitor

For the AVCC pin decoupling:

1 uf Capacitor for the main decoupling

10-100 nf Capacitor  for decoupling at HF frequencies

For the VDDIO2 pin decoupling:

1 uf Capacitor for the main decoupling

10-100 nf Capacitor  for decoupling at HF frequencies

On my board pads labeled C1,C2 are connected to the main (digital)VCC pin.

C3 is connected to the AVCC pin.

C4 is connected to the reset pin.

I should perhaps in the future at least add a capacitor pad for VDDIO2 pin if using a DB variant.