I don't have a IRToy, but the documentation for IrScrutinizer says that you need to plug the IRToy into a USB port, start IrScrutinizer, go to the Capturing Hardware pane, select IRToy tab, select the correct port, click Open.  Then you can click test or go to the Scrutinize Signal pane and click Capture.

I don't think you need to involve LIRC in any way.  It's probably best to ask other questions at hifi-remote.com.