Hi,
In order to run the web service unit tests, as you have probably gathered, you first need to run the WebServiceBootstrapSystemTest. This creates a node store and a couple of folders and documents that are then used by the web service tests. This prevents your main SpacesStore being polluted with test results. It doesn't require any additional configuration.
Once run, you should start the repository in the usual manner (as if you where going to access the UI). With the repository still running you can now execute the web service unit tests by running the WebServiceSuiteSystemTest test suite.
Also you will find some further examples in the samples package, that also the require the repository to be running when they are executed.
Hope this helps,
Roy