NDSTS and NDSHV are GUI based apps so you just load up a rom and extract or import files normally using the mouse. While NDSTool can pull an individual file from the rom it is usually easier to use one of the others.
NDSTool is slightly more powerful as it is able to completely rebuild the file system (the others need to replace files of the same size), it is however command line based which can in theory make things harder:
Disassembly
I have included a rename command so you can simply put the batch file, the uncompressed rom and ndstool in an empty folder and run the batch file to disassemble the rom, if you have the rebuilding batch file as well you can copy that across as it will not affect the process.
Code:
rename *.nds x.nds
ndstool -x x.nds -9 arm9.bin -7 arm7.bin -y9 y9.bin -y7 y7.bin -d data -y overlay -t banner.bin -h header.bin
Now you just have to run this batch file (it is essentially a program so just double click it) and a DOS prompt will flash up wait 30 odd seconds (depending on rom size) and the DOS prompt will close and on your drive in the same directory as the batch file and ndstool some folders will appear (data, overlay...) and a bunch of files will appear, now you can edit the rom as you please.
Rebuilding/compiling:
Code:
ndstool -c xmod.nds -9 arm9.bin -7 arm7.bin -y9 y9.bin -y7 y7.bin -d data -y overlay -t banner.bin -h header.bin
When you run this from the same directory as NDSTool and a previously disassembled rom it will make up a file called xmod.nds.
Either way you can now get at the sound_data.sdat file to modify it using the methods I suggested above. The XML file is just a copy of the spreadsheet I made up with all the individual file locations and their size within it (files have some junk bytes between the end of the file and the start of the next) which you can use to help when repointing or deciding upon a place to chop the file.
As for just replacing the soundfile (deleting rarely if ever lets the rom run again) grab one from another rom (goldeneye is a good bet as it is only a couple of KB) and then replace the original sound_data.sdat file before rebuilding.