Question about Suica and transferring.

This might be a very dumb question but I had some trouble earlier in my Japan trip and messed up my Suica (didn’t tap out), although I got it fixed. I just want to clarify something. I will give an example, If I enter Shinjuku Station and take the Chuo Line to Tokyo and then transfer to another local line, where do I tap with Suica?

1. Shinjuku when entering chuo line
2. Tokyo gate to the other local line

Or

1. Shinjuku when entering chuo line
2. Tap in and out at the exit to finish the trip
3. Then gate to the other local line