You can pick anything you want to change as long as you change at least one thing on the car for it to count. Now walk up to the area again and press to open the garage menu, now select which car you want to customise and press the Customise option. Once you've hijacked a car drive into your cribs garage and into the store area and press to store the car.
I found the easiest method was to steal cars from outside one of your cribs/safehouses and take them into your garage and customise from there and I suggest using the quick hijacks ( + ) to steal the cars to save some time and to work towards Bo-Duke-En in Saints Row: The Third.
You can easily attain this after getting your first safehouse (Shaundi's Apartment) unlocked not long after completing the second mission (which unlocks The Welcome Wagon in Saints Row: The Third).
