1) Configure passthrough: Settings/Audio/Digital output format = Passthrough (otherwise everything non-DTS is transcoded to the highest detected Dolby level of the connected devce - you dont want this).
2) Disable sound modes: During playback press Options (*)/Sound settings/Customize sound modes = Off
3) Prime requires a 4K or HDR configured display device for Atmos (Atmos is only encoded along with 4K/HDR streams) - this means Settings/Display type = 4K TV, 4K HDR TV, 4K HDR10+ TV, or 4K Dolby Vision TV (Automatic or manual configured). Prime will not output Atmos with a 1080p HDR setup on RokuOS due to no configuration option (other platforms allow 1080p HDR configurations, and will output Prime Atmos, e.g FireOS and Android/GoogleTV OS devices).
