I created a Eclipse plug-in project by selecting a plug-in template provides by the eclipse. Then i ran the plug-in it opened another eclipse and the plug-in executed there.
When you run a plugin (Run As > Eclipse Application) Eclipse starts a new instance of Eclipse including your plugin and uses a new workspace. This enables you to test the plugin without damaging your main Eclipse installation and workspace.
If you want to run the plugin in your main workspace you will have to export the plugin and install it in your main Eclipse.
If you want to run your plugin as part of an RCP you can set the application or product launched in the 'Run > Run Configurations...' entry.
For example:
Here I am running a product called 'greg.music.e4.rcp.product'