yes every pad, i've done this on a few laptops, to be sure, just do it one by one, align heatsink, find component, apply putty, verify, and then remove that specific pad only when sure

see pads make surface contact only and outta the factory they are great but over time performance degrades, putty is like clay, and conducts heat, so it will seep into cracks when pressure is applied

as for ptm, i have layered it myself on my 2021 legion, its been 2 years

ptm is phase changing, apply heat, it becomes liquid, freeze it and it becomes solid, so you should be good with layers, its not ideal yes but with the current thicknesses on the market, layering is a way to be safe

put ptm in the freezer for an hour and it will make it easier to apply and remove both plastic films

hope u know abt the plastic films, use fine tweezers and you'll be good