Chosen Solution
Which one of the two heat sinks has the GPU underneath it? Should I reapply the thermal compound on both heat sinks while I’m at it?
I would use the CPU fan replacement guide to point to which one is for the CPU. That guide is here. Personally if you are having heat issues I would reapply thermal compound/paste to both the GPU & CPU. You do not apply thermal compound/paste to the heat sink, it is applied to the processor - thin as possible, yet still covering. A rough guide for applying thermal compound is here. I recommend using the Arctic silver thermal compound/paste available here.
