If you are not sure when to use the basecoat....you may want to rethink the whole touch-up approach. Someone who understands and is patient can touch-up a spot until it's height exceeds the remainder of the finish, then using fine sandpaper (I use 1500 - 2000grit) bring it back down,carefully, and then buff with the appropriate pads and products until the touch-up just goes away.
If you have never done all these steps. Take a piece of scrap and practice, a lot. Until when you get done buffing, the repair is no longer visible. Then try it on the bike.
Most scratches do not go thru the base and you will only use the mid and top coats to touch-up.