The readme is extremely vague and un-user friendly, but from what I understand you literally put the "cpufreq" file in the same folder as the GPE executable, and rename it to "cpufreq --freq 600"
It's not a program you launch, but a little extra instruction that you install in the program folder, you put in your gpSP folder or your loquake2 folder, etc.
...Am I right or wrong? I honestly don't know.
Scratch that, I clearly have no idea what I'm talking about.
If and when gMenu2x is ready to overclock your apps for you, that'll be the easiest option.
It's not clear to begin with that to use the program, you need to have some basic unix/linux knowledge.