Well, it's a bit more complicated than that. Essentially there are three different things that are controlling your processor, the kernel, a 'governor' and an overclocking app.
The kernel just determines which speeds are available to the processor (just think of it as a list of numbers). You can specify the minimum and maximum speeds the kernel allows whilst flashing it, but once that's done the kernel won't change.
The governor is basically there to tell the processor which speeds it should be using. If you're doing something complicated with the phone, the governor tells the processor to speed up and vies versa. The more modern governors are very good at managing this and you won't even notice them changing the speed. Flykernel comes with a governor called 'smartass', which won't let the processor go above 350MHz with the screen off, saving you power. When the screen comes back on it will immediately let the processor jump as high as necessary.
Overclocking apps, such as
SetCPU, are apps that let you set your own min/max speeds and pick which governor to use. You can add rules to change the available speeds depending on whether it's plugged in, temperature and so on.
So whether you flash flykernel or stick with villain's kernel, essentially all you have to do is set your min/max in SetCPU and pick the right governor.