A TV can take input from one HDMI device at a time. Having two devices with overlapping functionality is not an issue for the devices or services. You can switch between devices by selecting a different HDMI port for input on your TV (or AV receiver).
Choose any free HDMI port with matching feature and bandwidth specification.
If one of your HDMI-in ports is marked DVI, then that will not carry audio. It is best suited for connections with computers.
If one of your HDMI-in ports is marked ARC, then that is intended for connections with audio equipment (e.g. receiver or soundbar).
For Apple TV HD, use an HDMI 1.3/1.4 port or better.
For Apple TV 4K, use an HDMI 2.0 port or better.