If the flash drive always comes up as Drive E:\ (or whatever). You should be able to install BlueJ to that drive. Java needs a path to the JRE and another path to the /bin inside the Java1.6_uxx folder.
NetBeans maintains a database of the paths to those locations on the hard drive. Maybe BlueJ does too. If not, you will have to learn how to compile and launch java code with the path variable.
example...
E:\ javac -classpath \Java1.6_10\bin MyCode.java
You may have to set something like my example in BlueJ
In other words, know how to navigate to folders on a hard drive using DOS commands
C\:> cd E;\
E\:> \Documents\resume.txt