JavaBeans are simply Java classes that conform to the bean architecture and aren't anything magic. Normally they serve as containers for either data or services, so they generally aren't executable themselves. Instead a control class (containing the main method) is executed and that class creates and invokes other classes (JavaBean or otherwise) as it needs to.
Eclipse doesn't handle JavaBeans any differently than it does any other Java class.
An IDE is no substitute for an Intelligent Developer.