Touch up paint

[zero4]

So I have scratch on my car that I want to fix. I was stupid enough to close the garage when the lift gate was open on my car. It's gone through the clear coat but likely not the base coat. If I were to use touch up paint, is it better if I use clear? I have the Dr. Colorchip matching paint but wondering if using a clear touch up paint would be better. Thanks.

[Crispy]

Can't do much without pics.

Clear is clear so won't change colour.