If you haven't started JChemPaint yet, you can do this using a Java virtual machine, by typing
java -jar jchempaint.jarin the directory where the JCPCDK_Home/jchempaint.jar is located, or, on Windows, by double clicking on the jchempaint.jar archive. By default, JChemPaint will start in multiple document interface (mdi) mode, you can see multiple molecules inside one frame. By using
java -jar jchempaint.jar sdiyou get the single document interface mode, every structure has a separate window.