What leads you to believe that Windows isn't using all 6 cores?

Not all programs are good at using multiple cores to improve their performance, so it's not surprising that some programs are benefited more by overclocking.

To check if Windows sees and is using all of your cores:

 1. Start -> type Task Manager, press Enter.
 2. If you see a More details button in the lower-left, click it.
 3. Click the Performance tab.
 4. Click CPU.
 5. Verify that "Cores" says 6, and that "Logical processors" says 12.

It's the application which dictates how your cores are used. Lots of everyday applications won't be properly multithreaded because there is no need or the devs were lazy.

Overclocking it will make everything run faster regardless of its threading. What exactly are you running?

...i remenber to all just a simple think:
the OS, windows, linux iOS etc etc,
give users the possibility to run programs who use multithread...
but in last istance, the use of 2 ore more cores, it depends on how the software was programmed.
if the software it is programmed for a multithread environment, OS will use it if you have a multicore/threads CPU...
otherwise not...