This is my first Eagle layout so all the help is much appreciated.
This is designed to control an led strip "mosi & sck", programming it via MKii / AVR Studio 5 and powered by 4 rechargeable batteries so I didn't think a regulator is needed. I placed text on the pins for definitions, I know not to keep them there.
Add a polygon to each layer (Draw:Polygon) and Name it GND. Get rid of the ground traces.
I would add 0.1uF cap to VCC pins on all 4 sides of the chip, similar to how you have 1 one for Aref.
Your pin arrangement for ICSP is odd - you will have to make an adapter cable to mate to the 2x3 header on the Mkii.
The Mkii does not power the board but needs to receive the Vcc so it knows what the voltage being used.
Thus you need to bring power & gnd into the board while the Mkii is plugged in.
I don't know that the Mkii will reset the uC correctly thru a cap like that. I would connect RST direct to pin 4. The other side of the cap is normally DTR.
If you are not downloading sketches via Rx/Tx you don't need the DTR cap.
'644 seems like overkill for the application, do you need it for the memory size?
Yeah, have noticed that sometimes you need to add a manual trace. Could be the ground plane squeezed around the hole is too thin.
Try moving the resonator to the right some.
You can also try adding a via near there, name it GND also, to connect the top & bottom planes.