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I use a ESP-12E, where all the pins are broken out and nothing is connected on the board itself.

Online I found different ways to connect the pins GPIO16 and RST (RESET) to allow automatic wake-up from deep sleep:

I also found someone using CH_PD ("EN") pin instead of RST, but I see it's not the preferred way.

What are the differences between the two alternatives I listed?

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Most of the people face the problem while connecting them. The issue is that GPIO16 provides a strong HIGH during deepSleep and your external reset from Serial-TTL is fighting to make a reset, but loosing, the GPIO16 is the strongest. To avoid such issue, simply replace the wire by a 470R or 1K between GPIO16 and RES, which will allow the Serial-TTL to win. (you can also use a schottky diode with the cathode on GPIO16 side)

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I'm using and ESP-01 with CH/PD tied to Vcc with a 10K resistor. That keeps the ESP running in deep sleep. To wake it up connect the CH/PD to ground through your switch. My switch is a reed switch and this method also seems to debounce the reed switch.

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