Except under exceptional circumstances (see note), the organisation of your code will have no impact on the final product. (contents of the code are obviously a different matter)
So with that in mind you should organise your code as you would any other project.
With that said, the following are fairly typical:
If this is a processor that you've worked on before, or will be working on in the future, you will usually want to keep a dedicated hardware abstraction layer that can be shared between projects in the future. Typically this module would contain items like routines for managing any uarts, timers etc.
Usually it's reasonable to maintain a set of platform specific code for initialisation and setup that performs all of the configuration and initialisation up to the point where your executive takes over and runs your application. It will also include platform specific hal routines.
The executive/application is probably maintained as a separate module. All of the hardware specific code should be hidden in the hal (as mentioned above).
By splitting your code up like this you also have the option of compiling and running your application as a simulation, on a completely different platform, just by replacing the hardware specific code with routines that mimic the hardware.
This can be good for unit testing and debugging and algorithmic problems you might have.
Exceptional circumstances as might be imposed by unusual compiler restrictions. eg. I've come across some compilers that expect all interrupt service routines to be compiled within a single object file.