Hey, sounds like you got this thing up and running in your car!

Obviously, EMSC can only interpret stuff from WinLirc if it is running..., so you need additional sofware independent from EMSC, such as Girder and some others listed in the WinLirc site) that allow you to perform certain actions (start program x, shutdown the machine, etc.) when you press certain buttons. You can use those no problem in coexistence with EMSC. Perhaps Quit, when chosen from the menu instead of pressing the q in the keyboard, should ask for confirmation...