Just arm9 or overlays as well? I have seen games include everything and end up with hundreds or even thousands of overlays before but all in the ARM9 (save for sound I assume) is new.
Back on topic..... with a hex editor usually. If they are packed into/included in the ARM9 it is probably not going to be with a proto filesystem or anything like that and will tend to be referred to directly by memory addresses (which you will also have to fix/change* if you make the file bigger, you also then get to juggle memory and possibly find some free space in the memory to hold things**). If they are known formats or conform to the normal DS standards (magic stamp plus file length) then you usually have a nice start of file indicator and a length of them which helps immensely, they tend not to be doubly compressed either (only binary compression across the whole binary as it usually is) but it might happen in the case of something that has to get to the VRAM instead.
*dynamic/calculated pointers are also a possibility here so you may have to run/observe the game to make sure this does not happen.
**I occasionally fish nice long wifi error messages in several languages out of binaries, this can provide a nice bit of space for you to reclaim.
In short it is actually closer to classic ROM hacking really (everything is known to the game at fixed locations and probably memory mapped too, you have to figure out the pointers to them or hope you do not make the files bigger) but with the twist that expanding the "ROM" is a nightmare most of the time when the "ROM" is a DS binary. Trying to find free memory at runtime on the DS.... well there is at least a tool to help you
http://gbatemp.net/threads/unofficial-desmume-build-unused-memory-finder-tool.349332/ or if you prefer a slightly more manual methods then DSATM has an option to patch the ROM to change all unused memory to DEADBEEF (
http://filetrip.net/nds-downloads/utilities/download-dsatm-434-434-f27609.html and that is the last version with the functionality, later versions dropped it).
If you really want I have been toying with the idea for years but never put it into practice really. If you can get a GBA slot device then you gain up to 32 megs of very fast memory mapped memory, possibly even writable if you work at it. Somewhat larger than the DS' 4 megs.