The base clock is 3.5GHz but that CPU can boost up to 3.9GHz on a single core (IIRC), and 3.7GHz or so on a couple of cores.
It's a designed use-case, and there's nothing to "fix".
Except my cpu is still only using 2 of its cores
If that's truly the case, that has nothing to do with clock speeds.
How are you identifying it to only be using 2 cores?