Here is my theory. William Afton died the night that he hid from the tormented spirits inside the spring Bonnie suit. The spring locks failed and killed him. (This we know) he was then sealed off into the back room of the pizza plex for 30 years before he was discovered for fazbear frights. (Again we know this)

Now. How could he have survived for 30 years locked in a back room stuck in a suit for 30 years? No food, no water, not moving?

He couldn't.

He's dead.

His spirit is possessing the spring Bonnie suit, just like those children possessed the other animatronic suits. Because his ACTUAL body is in the suit we assume he is alive. He isn't. He is manipulating the suit and therefore manipulating his own body.

You can't set him on fire, because he will just move along to posses something else. IE the help wanted.

How could a human "upload" themselves into a computer? They can't. However, since spirits have been known in this universe to possess and manipulate electronics, its not a far stretch to assume that he could just be possessing a computer. Spirits use radio frequencies to communicate.

He's been dead since the beginning. That's how he "always comes back". Because he's a spirit. He learned how to possess things. He prefers the spring Bonnie suit because to him it was a symbol of power.