Do you have a schematic to go with that? This layout raises some questions - maybe you are just starting.
Where is the RF transmitter? Where are the connections to whatever the board receives data from to send out? Is there a place to connect an antenna for the RF transmitter antenna?
Is the big chip to be installed in a socket so you can pull it out to reprogram it?
I would call the battery connector something besides VCC1 - VCC usually indicates the power after it goes thru a regulator, not before it.Maybe call that BATT1 instead.
Most regulators would also like to have an input capacitor and an output capacitor.
I would also design in some pads to give yourself some other power connections - like skip the regulator, run from 6 AA batteries for example - with 4.5V going to the atmega and 9V going to the transmitter for better range. Or if running at lower frequency, say 8MHz, run off 2 LiPO batteries - 3.7V to the atmeage, and 7.4V to the transmitter.
I have a remote control using this Rx transmitter MO-SAWR, WRL-08946 TX from Sparkfun, transmits fine from 3.7V as well over.
J1 - this is going to the transmitter? Pin 5, (Arduino D3?) is to be your output pin?
Why not add a 2nd row of holes adjacent to the big chip, connected to the pin next to it, give yourself some flexibility for making other connections?
Yes, the picture depicts looking down at the top of the components - the little square at the upper left of the big part indicates pin 1.
My remote, runs from 1 LiPO 1000mAH battery, plug into 5V to charge it up. Development was done with 3 AA batteries & no charger.
Goes into sleep mode after a key press.