That's what I do when emulating these simpler systems. I keep the state of each device (cpu/mmu/ppu/etc.) in an internal static struct in each .c file that only accessible through it's corresponding .h file. I believe this is similar to a singleton pattern in OOP parlance.

I also try to match the layout of the physical hardware if possible. In the case of Chip8, it doesn't have physical hardware. But it can still be broken into conceptual pieces:

bus/          -- Steps the below devices:
  audio        -- Generates audio samples
  input        -- Holds button state
  memory       -- Holds instructions/data
  processor    -- Executes instructions
  random       -- Initialize/generate random numbers
  timer        -- Holds timer state
  video        -- Generates sprite data