Ardupilot software on custom board

Hi all,

Long time lurker but new member... So first off thanks for everything so far :)

So a new project I am working on is a new sensor platform based on an rather small autonomous rover. For this at the moment I have a pixhawk and a raspberry pi connected via uart. However this is far too bulky for my liking and I would like to produce my own board to minimise cost. I already have ever a Linux sbc on there running on a at91sam9n12 chip, and am now ready to start on the rover hardware. I want it to be separate to the Linux and on an arm chip similar to how the pixhawk one does it.

Here is where I come up short on the low level knowledge of ardupilot goes. Pixhawk has the distinction between fmu and io. I ideally would be combining these into a single STM32F7 series chip. From my understanding from others, I would have to write the HAL and then flash it. However my understanding of the flashing process is limited, especially as I cannot see a distinction between fmu and io. 

The other option I have is to have the two processors as with pixhawk, however as with above, I do not know about the process in order to load the firmware on the chip.

Any help with this process would be greatly appreciated :)

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