Keyless Entry system

Hello, I purchased this car about 2 months ago. The problem is the original remote key fob which I only have one, worked okay for about a month then it started working sometimes then not at all. I checked the battery, it read 3.6v okay, next I bought a new remote key fob online with matching numbers on the old one, when I put the car in program mode and followed program instructions the door locks cycle (lock/unlock 2 times) it did not pair. So, I changed the door control receiver module which I got the same results not pairing what could the problem?
Question 2.
if I install a Car Security System Alarm with Keyless Entry, will the new system Keyless Entry use its own signal to lock and unlock doors, or does it use signal from the Toyota system?