I am not sure I understand the question. In the Flash Memory Map is a set of sliders. You can slide them back and forth. The S/W ensures that you do not go over 4MB. You must, of course remember the following:
NVRAM takes up 64KB. This is non-negotiable.
The boot loader (unless modified) takes up 64KB. This is non-negotiable.
If you do not want a backup image, set it to 0.
I believe by default, any FLASH space NOT taken up by the application, the bootloader, the backup image, NVRAM is given to the file system.
What else do you need?