(I try to give a short summary but probably you should read the manual!)
Did you already create listening rooms and presets?
Before you can do anything with your PRIRs you have to create a listening room in which you select virtual speakers from your PRIRs. And then select a preset in which you selected such a listening room.
In a listening room you first set the listening [edit:room mode, sorry], like 2.0, 5.1, 7.1, 7.1.4, 9.1.6 etc.
And then select speakers from your and/or other/factory PRIRs for all available channels.
If the dolby upmixer is on then the listening mode that I mentioned before determines what format you are upmixing towards.
You will have to make different listening rooms for Atmos (for all dolby formats) and for PCM (for all PCM input signals. the analog inputs are also considered PCM signals in this context). (In the future when DTS is added you will also need DTS listening rooms).
In each preset you can define an Atmos listening room, a DTS listening room and a PCM listening room. The A16 will automatically select the listening room in the active preset based on the input signal (dolby, dts or pcm).
In 16 channel mode (or with a 16 channel version of the A16) you will have to make a seperate preset for 5.1.<something> in which you use speakers from your 5.1 PRIR (at least the surounds, at slightly different positions compared to 7.1). In 24 channel mode, which I have no experience with, you probably have listening modes in which both the surround positions (90 degrees and 120 degrees?) are available, maybe you don't need a seperate preset for 5.1 based stuff, I don't know yet.
Whether you will like a combination of speakers from your own PRIRs and other PRIRs depends on how the speakers from the other PRIRs sound to you.