The most practical way to do in system programming between multiple devices when you want to use off the shelf existing software and/or programming pods is to do the following things:

1) Separate the programming interfaces from the application interfaces.
2) Provide individual programming connection interfaces for each device.
3) Consider using devices that have a low pin count programming interfaces such as SiLabs parts which have the C2 interface that just takes two pins (one of which is also the RESET pin.

If you want to combine the programming interfaces and the application interfaces then you are invariably set to be writing your own code. And in particular if you want to make this job have the least hardware impact and cost on the design you are looking at the need to install bootloader code into each microcontroller.

In any case I could suggest that using the same device or same device family for all the MCUs in a given joint multi-programming structure will also make the job more straightforward and less work. Especially if you go down a path to be writing your own code.

Michael Karas