You can use either method.
If you prefer to have a set diet plan, make sure you select that option when setting up your profile. That way you know exactly what you need to eat for breakfast, lunch, dinner and for snacks. This works for some people, especially if they're new to weight loss and aren't sure what they should be eating for a balanced, healthy diet.
If you want some flexibility, if you prefer to choose your own meals, or if you have a dietary requirement that isn't catered to in CK's options (for instance, I'm a vegan and they don't have a vegan meal plan available) then you can choose to enter your own foods. This option is good as a way to learn about comparative calorie and fat values of foods. For instance, if you're wondering whether to have a Subway veggie delite or a falafel for lunch you can enter them both in and see which one is the better weight loss option.
You can enter your own custom foods and exercise if they're not in the database. If the search comes up with nothing there will be an option to create a custom food. Provided you have the nutritional information of that food you can enter it in yourself, then save it as a favourite if you ever plan to have it again. Next time you search for that food it will come up from your favourites list so you don't have to enter all that data again.
If you need any more help just let us know!