if they batteries that are in your key dies will that stop your vehicle from starting?

No, just keeps the FOB from working, car will still start with key.

I'm assuming you mean the remote-starter installer stuck a copy of the master key inside the vehicle as a means for bypassing the PATS (passive anti-theft system)? If that's the case your vehicle has been without anti-theft protection ever since. If you ever get a car/truck stolen, the insurance company asks if any remote-starters have been installed and how they were installed. Having that key permanently hidden in there for the remote-starter is a cheap way to bypass the PATs but it will not keep your car from starting if a battery dies in the FOB.