Confusing transfer shinkasen from kyoto to tokyo and then JE keiyo line to tokyo bay…no gates to enter new JE ticket?

Is my transfer somehow included in ticket from Kyoto?

I got two tickets when i bought them in kyoto. When I entered the tracks i got both back. After making it to Tokyo and passed one gate we got one back and followed directions for JE keiyo line, but didn't see gates or machines where to buy tickets.
Is this transfer included somehow?

Trying not to get in trouble when trying to leave in tokyo bay