In addition to the quick-start text file included in the release package, I thought I could show you a quick and dirty way to make Nijuu make some noise so you'll at least know it's working.
With the template files copied, named with the name of your choice (and don't forget to edit the SONG_NAME variable in the .NIJ file), open up the .SNG file in a plain-text editor.
Scroll down to where you see the sequence named "S1" (it says "Blank sequence for Drums" just above it).
Go down to the line that reads "db 0" and change this to "db 1,2,1,2".
Save the file.
Go to the command line/shell as described in the readme.txt file and compile the song as instructed.
Open the .NES or .NSF file, depending on what you built.
It should be playing a simple kick/snare drum pattern.
Read the manual, carefully. :)