If you want to leave setEl intact what you could do is have your methods return an object of type matrix that you create and put your summed values into (same idea for subtraction). That way your counts are right and it might even be a bit cleaner than overwriting.
Otherwise, decouple setEl and the nent counter and have a "shell" method to use from main() that calls setEl and then increments the counter when it's necessary (so in your add method you would call the plain setEl without the counter).