While there are several apps for managing your CPU speed with an overclocking enabled kernel, SetCPU is the most popular. When launching it for the first time, Superuser will prompt you to allow root privileges. If it does not, your device is likely not properly rooted.
SetCPU’s main screen is fairly straightforward. It has two sliders for setting your minimum and maximum clock rates. Your choices here are dictated by the CPU table provided by your custom kernel. Most popular kernels are fairly conservative with their maximum values, and most devices can actually achieve them; however, it’s best to work your way up slowly, testing your device through each step with something like a benchmark or demanding game. If it freezes or crashes, you know you’ve gone too far will have to settle for a lesser overclock or increase the voltage.
The Voltages page is best left alone unless you are confident in what
you are doing. Ideally, you want your voltages to be as low as possible while keeping the system stable. This is one way to conserve power. Most custom kernels will already have these values optimized, so you should not have to change them. If you’d like to adventure into the realm of voltage modding, it’s a good idea to peruse your device’s page on XDA Forums to see what ranges are safe.
The Profiles page is another way to conserve power. You can use it to create conditions for specific clock and voltage settings. For example, when your battery is below 25%, you can have SetCPU underclock your CPU’s maximum speed from 1GHz to 800MHz. Some custom kernels have profile-like conditions built into them already and do not play nicely with SetCPU’s profiles enabled. Read your kernel’s notes to see if this is the case with yours.
CPU Governors and IO schedulers are the last significant settings you’ll need to worry about with SetCPU. There are two on the bottom of the main page. The CPU governor is on the left, and the IO scheduler is on the right. The list of choices will vary depending on which governors are packed with your kernel. A great explanation of the different CPU governors and IO schedulers can be found on XDA Forums.