That's because you actually need to run the program from a terminal window, because it has no graphical frontend (yet).
Just press the Windows + R button combination, type in "cmd" and press Enter. Then, use the "cd" command to go to the directory where the program is stored. For example:
cd "C:\MY_DATA\3DS Stuff"
If it is stored in a drive different to C:, then use the "/D" specifier, like this:
cd /D "F:\files\programs\3DS Stuff"
Alternatively, you can just install something like
Clickie, right click the directory where you saved the program, and select the "Open MS-DOS Prompt" option.
Afterwards, just run the program by typing in its name. If no parameters are given, the usage screen (quoted in the first post) will appear. The information explained in there should be enough to make you understand how the program works and the meaning of each option/parameter.
If this is the first time you are configuring the Second EmuNAND, then you'll want to run the following command:
3ds-dualnand -2 -i NAND.BIN boot.bin
Make sure both NAND.BIN (NAND dump to be used as the Second EmuNAND) and boot.bin (from the Palantine CFW data) files are present in the same directory where the program is stored, and that the SD card that contains an already formatted GW/MT EmuNAND is inserted, and press Enter.
Keep in mind that doing this will wipe the current partition table from the SD card. Backup your files before running this command.
When the process is completed, restore your files to the FAT32 partition and copy the data from the Palantine CFW to the root directory. Then, rename the Launcher.dat from the CFW to MsetForBoss.dat, and replace the boot.bin file with the one stored in the program directory (now modified).
Finally, just use the
ROP Multiloader with your NDS Flashcard to swap between ROP chains each time you want to load a different EmuNAND:
"Gateway Launcher.dat 4x" -> First EmuNAND (GW/MT)
"Homebrew MsetForBoss.dat 4x" -> Second EmuNAND (written by the program)
Hope it helps. It is still way easier to do for people that are unfamiliar with the info explained by nop90 in his tutorial.