How to setup CIS for minimum breakage and maximum diagnostic resources?

I put CIS on my mom’s computer a while back; but then it started giving trouble with some programs (I don’t remember all of them, but I think one of them was a thing to update or install Microsoft Office); after a while having to frequently come back and do manual fixes I taught her about game mode, but she misunderstood the purpose and just left it on all the time, and now I found out and explained to her why that isn’t a good idea she’s considering having CIS removed and install something by some competitor.

Does anyone know of a guide to setup CIS in a way that will reduce the odds of it breaking the functionality of programs to a minimum while still keeping the machine reasonably safe, and provide as much details about what it is doing as possible to make it easy to diagnose when something does break? Or to put it another way, I wanna have Comodo keep my mom’s machine safe without breaking stuff, but also making it easy to figure out what it did when it inevitably breaks something.