This link here would give you a bit of information.
A System application is NOT an application which is signed by the OS’s platform signatures. This is a common mistake believed by many and we shall come to this later on. A System application is merely an application which is placed under /system/app folder in an Android device. An application can only be installed in that folder if we have access to the OS’s ROM (system.img). The application is placed under /app folder after the ROM has been extracted. A device which loads the custom ROM will have the new System application added. The benefit of a System application is that the application cannot be removed from the device (cannot be uninstalled by the user). This is only because /system/app is a read-only folder.
http://ricston.com/blog/explaining-behavior-android-application-system-apps-nonsystem-apps/
As for updating your app through the play store, I am assuming you should be able to do that without any problems, if the app is on the play store, and you use the same signature every time. It need not be the manufacturer's certificate, but it's better to use that certificate to sign your app.
So, the only thing that you need to ensure is that, while building the ROM, the manufacturer puts your apk into the system folder, and it should work.