How can I install SuperSu on a pre-rooted Android head unit?

I am working on a pre-rooted Android head unit. I can do "adb root" or "adb shell su" using wifi adb. So there is root access and Su binary on the device. But I can't use root applications because there is no app to grant root access. I have tried installing supersu or superuser on /system/app. I made it install the apps but they say "device not rooted" when I try to run them. So how can I make supersu see my su binary?