The tools panel simply contains all the basic functions any java ide needs. It has the the compile, run, run applet, and etc buttons on it. You simply drag'n drop a project, package, file, or class onto one of the icons and it will do the assigned action to project, package, file, or class.
Pressing the buttons pulls up a dialog that allows you to cofigure options for that function. You can assign the program that does the compiling and what command-line options you want that program to have.