I agree that you shouldn't be deploying to the BizTalk.System application.
To check that you are deploying to the correct place, open your BizTalk project properties and click on the 'Deployment' tab (I'm making the assumption above that you are deploying locally, in which case the BizTalk Group Server and Configuration Database should already be set).
Under BizTalk Group, set Application Name to 'Test Application' (this can be changed later to something more meaningful); ensure all of the other boolean properties on the Deployment tab are set to true, with the exception of the Enable Unit Testing property.
When you now deploy the project from Visual Studio (by right clicking the project name and selecting 'Deploy', the new BizTalk Application will be created and the project deployed as a resource to that Application. Watch the VS Output window to check that they deployment is successful.
Once the deployment has completed, open the BizTalk Server Administration Console and expand the Applications node, you should now see a new application called 'Test Application'. If you expand the new app and take a look in Resources, you will see your recently deployed project.