Mostly it is ok to change just fsr scale in yml.
What I generally use:
Pitool ss1, Steamvr ss1 - that is 3160 pixels vertical.
In demanding games I put FSR scale to 0.84 - that make game rendering on 2860 pixels vert., and then fsr scale that to 3160 - that is what I see.
In non demanding game I use same pitool and steamvr settings, but fsr scale is 1.4.
That makes game to render on 3160 pixels vert., and fsr scale that to 4424 pixels vert.
Just sometimes I use other settings, i.E. for IL-2 currently I have Pitool 1, steamvr generally ss1, Steamvr per game ss0.84, and then I upscale with fsr high (like 1.3).
It is just for this game, as low initial resolution will show me small dots in a distance, and high fsr scale later will give nice picture too.
PS: scale is not same for steam and fsr; steamvr 0.5 will give half of total pixels, and fsr will give half pixels on scale 0.77.
Just like oculus vs steam supersampling scales.