Design choice single or multiple chips

[areuz]

Hey,
I'm working on a decentralised set of devices that are going to communicate using a RF69 transceiver - a sort of home automation system, but not quite.
At first, I wanted to make a comms. module, with the transceiver and an AtMEGA (328p or less powerfull). Now I realised that I might need something more powerful - an ARM of sorts (like a SAM4N or SAM4L from Atmel).

So, I wanted to ask, what is better:
1. Running all of the communication code (message relaying, parity checking, encrypting.. etc.) and the main code (depending on the device's purpose) on the Atmel ARM.
2. Or running the comms. code on an ARM, and having the AtMEGA just occasionally receive a message directed at it, for.. switching something like a relay, logging temperature from sensors, etc.

I don't yet fully understand how I would run both comms. and main code on a single chip - and I dislike the idea of a interconnected mess of thousands of lines of code being rewritten every time I flash the chip. I know that parallelization exists, but it has it's disadvantages with the less powerful chips... and I would still have to have the code as a single giant program, wouldn't I?

What I mostly care about is the power consumption and ease of debugging, because debugging wireless devices is a nightmare.