FLIRC or HDMI-CEC

just got a harmony remote but not sure if i should get a flirc or pulse eight’s usb hdmi-cec. right now i have my cable box and chromebox going through my onkyo receiver to my lg tv. the receiver and tv have cec but not my cable box or chromebox. not sure if it would make more sense to go with 1 over the other. lets say im using my remote to watch cable,if i turn on kodi and the inputs change do i need to tell the remote that im using kodi now or would it control kodi with the correct buttons?