Man, i'm researching for your problem. I want resolve it as soon as possible. By the way, you can try to do the following:
put ndstool.exe in your user folder(ex: X:\Users\TheUser\ndstool.exe );
then, run cmd(command prompt). Type ndstool.exe and read all the informations about ndstool, and how you can do your work fine(or if you can't, it depends).
Make sure your \tmp_[romname] is in the same folder as ndstool, or you must to write all the folders information(you understand what i mean when you read ndstool info)
If you encounter any problem, please write all the problems about emulators and flashcards(errors popups, blank/black screen, etc...). It can help us very much for try to resolve your problem