The basic controls for the CycleKart (apart from the steering wheel) simply consist of two pedals: One for Go and one for Stop. Layout is the same for a regular car, accelerator on the right and brake on the left.
You can use regular Go-Kart pedals, which are generally pretty cheap to buy and readily available. Or if you are feeling a bit creative you can make your own.
Pedal placement is of course very important. Too far away and you will not be able to reach them, which is also a consideration if you have younger (or shorter) drivers that will also be using the CycleKart. Too close and you're likely going to be hitting your knees on something, especially if you're taller than average. So taking the time to set the seat up properly and sit in your CycleKart to work out the ideal pedal placement is a very good idea.
Another thing to think about is the height of the pedals relative to the floor. This distance is somewhat dictated by the size of your feet, but a longer pedal also needs to travel further to generate the same output. You also need to feel comfortable and not have to strain your legs every time you drive, having to overstretch your foot to hold the accelerator pedal down will soon take its toll on your legs. So make sure that you can not only reach the pedals, but that you can comfortably operate them too. A heel rest is another good consideration as it will both reduce fatigue and can also help stop you front sliding around inside the CycleKart too much.
Connecting the pedals to the engine and brakes will also take some ingenuity. If you are using a hydraulic brake setup, the best thing to do is buy a long hydraulic line to enable you to mount the master cylinder in the optimum position relative to the pedal. The all-in-one brake kits that you find online that consist of a master cylinder and brake calliper connected by a ready made brake line are basically way too short as they are designed for minibikes, or regular Go-Karts. If you mount the calliper at the rear axle the master cylinder will end up somewhere next to your seat instead of at the front of the chassis. Whilst some have solved this shortcoming by making up fancy actuating rod arrangements to connect the pedal to the master cylidner, the first rule of engineering states that the more complex a mechanism, the more points of failure you have. It's simply much better to buy a longer hydraulic line to start off with. The same applies to the throttle cable as well.
Pedals should ideally have return springs mounted to them to ensure they return to the upright position. You should not rely on the return spring on the carburettor to pull the accelerator pedal upright via the accelerator cable. Likewise you should not rely solely on the spring in the master cylinder. If you intend to use GoKart pedals, ensure you buy the type that are supplied with return springs. Please also take not of the requirement for throttle return springs noted in the drivetrain article.