If you want to ensure that any version of a command is accessed from the command line then you make sure that the path to it occurs first in your PATH environment variable.

You have some kind of .profile (.bash_profile, .login, .kshrc, or whatever) in your login directory where you could specify this. You may need to set JAVA_HOME as well. i.e.
JAVA_HOME=/usr/local/jre1.3.1
PATH=$JAVA_HOME/bin:$PATH
export PATH JAVA_HOME
This depends on what shell you are using - likely bash (man bash)

-greg