it is a command line app, some use DSLazy as a frontend but I use batch files:
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 although I suggest you stick to the data directory as the others contain fairly vital data which is rarely that big anyway.
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 (and now probably modified) rom it will make up a file called xmod.nds.
You can leave the original x.nds file alone and if you are using it the disassembly batch file as well for this batch file will not cause ndstool to use anything else other than the files required to be included in the rom it makes up.
You can also include a few more commands like "del *.bin" and "rd data /s /q" and "rd overlay /s /q" after the ndstool section to tidy up after rebuilding but you will likely be deleting files and hoping the file gets small enough so you do not really want to get rid the files that quickly, many find it nice however if they can be rid of "useless files" if you make a batch file to go with your rip guide.
Now you can have three files (ndstool and the two batch files) which you can use to build and disassemble roms, I also keep a copy of goldeneyes small sound file to hand in the same directory as these three files are stored in for convenience.