If I set up conflicting registers, my code doesn't run and I go back and fix them like I would anything else. I have had mysterious problems from time to time that were traced to the fact that I SHOULD have set a register, but didn't. Once everything is working,
I carefully start removing the setups in small groups, all the while noting what the defaults are. If everything keeps on working, I
can remove more at my pace. If not, I go back and see why. I use only about 4 chips. None of my headers contains more than about 10 lines of setup - now.