The best way to do it would be to use a cocktail stick to apply the paint and just allow the paint to fill the gouge in the paint. This could take several applications as its better to build up light coats.
You should finish up with the new paint being slightly proud of the surface. You then need to flatten this off to the same level as the surrounding paint using very fine wet and dry (3000 grit soaked in water overnight). Use a small sanding block such as an eraser or cork and apply some washing up liquid to the paper. Carefully sand the touched up area until its flat.
Then use a cutting compound such as G3 to blend it in. Finally apply a coat of wax to protect the area.
If your paint is metallic like mine then this can be very hard to get an invisible repair due to the clear coat. Your never going to get an invisible repair because just like cracked glass you can see the crack despite the glass being level. Its the same with the touch up pens with the base coat and clear coat, i found that it looked a lot better but you could still see a sort of crack.
I think there are some better specialist kits on the market that have the clear coat mixed in with the base coat, i think these would give a much better result.
Regarding the Dr colour chip product it actually says on the website that it doesn't work well for large stone chips or scratches and advises to use "as is" which is basically just like a touch up pen.