How to make a Neural network understand that multiple inputs are related to the same entity?
It is not necessary to indicate this to the neural network (and not possible).  This is not part of how neural networks are typically used -- or part of how other machine learning algorithms are used, either.

I confess I'm not clear on why you think it would make a difference, but it doesn't matter: there's no way (that I know of) to do that, and it's not something people normally do.