If you are building them from commandline, as I assume you are, it doesn't really matter where you put them -- only thing that matters is that you define them in your classpath when building.
For example, if your lib file is in the folder 3D/Stuff/Lib and your app is in /3D you would do:
javac -classpath .:Stuff/Lib/theLib nameOfFile.java
Hope this helps.
-Rav