Currently the Tools support direct deployment of WTP Dynamic Web Projects, OSGi bundle and PAR projects to the Virgo Runtime from directly within Eclipse.
To deploy an application to the Virgo Runtime Environment just bring up the context menu on the configured Virgo Runtime runtime in the Servers view and choose "Add or Remove Projects...". In the dialog, select the desired project and add it to the list of "Configured projects".
Deploying and undeploying an application from the Virgo Runtime certainly works while the Virgo Runtime Environment is running, but you can also add or remove projects if the Virgo Runtime is not running.
Once an application is deployed on the Virgo Runtime Environment the tooling support will automatically pick up any change to source files -- for example, Java and XML context files -- and refresh the deployed application on the Virgo Runtime.
The wait time between a change and the actual refresh can be configured in the configuration editor of the runtime. To bring up that editor, double-click on the configured Virgo Runtime Environment instance in the Servers view.