The SQ blaster comes with LEDs which can be placed inside the cabinet, they have a sticky tape on them with which you can stick them onto the equipment. The SQ blaster itself can be used inside the cabinet too, as it emits IR too. So you can use the SQ blaster as extender as well.
I am not sure about the iOS app not finding your Vera, I use the PC software, that has no problems finding my Vera. I would think the iOS app should find your Vera as well, you will have to be on the same WiFi though