No, the manual does not tell you to replace your front speakers with the upward firing Atmos speakers. The upward firing Atmos speakers are used in conjunction with your existing front speakers and not instead of them.
These speakers are upward firing Atmos speakers and bounce the audio off your ceiling to create the effect of having ceiling mounted downward firing speakers so cannot be used as height speakers. They ideally need to be placed on the top of your existing front left and right speakers or positioned in a location that would approximate this. Your front left and right speakers should ideally be located at your seated head height. There should be a speaker configuration specifically for this type of speaker?
You need to use the FDL/FDR option and locate the upward firing Atmos speakers on top of your existing front left and right speakers. The suggestions to replace your speakers is made in reference to Atmos speakers that integrate the upward firing element and front firing speakers into the same cabinet.