With Visual PHPUnit you don't have to use terminal, so, you don't have to launch your test manualy.
You just have to select your test launcher which you have created and then click on "Run tests". But I think you are true, you can just run the library you specified. Maybe I have also to specify Config path.
You might be ok when you can convince it to use our phpunit.xml, which is in fuel/core, and which contains the bootstrap needed to initialize PHPunit for FuelPHP.
Or if it requires it's own xml, make sure you configure it like ours.
I decided to stop Unit Testing with Visual PHPUnit.
But now that I'm doing it with command lines I've got a new problem : I tried to use bootstrap_phpunit.php from Fuel/Core as my bootstrap to use but there is a problem : APPPATH, PKGPATH, COREPATH and DOCROOT are wrong in this file. And I've no idea what Path I have to set in each of these variables.