I have some interest in this:
Having allways on my old car:
1.If scratch was down to the bare metal used "l*c*i*e rust remedy" then base coat , then lacquer as suggested above.
Now however touch up paint is coming in water based paint varieties from renault which takes some getting used to ,for me anyway..
The recommended technique is to apply the base colour(on top of a rust primer or not ,it doesnt say),then after 15-30 min or so "sand down" the base coat using the cloth cap of the paint pot moistened with a little water.
This part is very vague,If you start too soon the paint wont have dried enough and you just rub away all the paint you have applied.
if you start too late ,it doesnt seem to reduce the paint height at all
If you get it right ,then you apply the lacquer and "sand that down" 48 hrs later just by normal polishing.
If your touch up paint is the older "non greenpeace" type good luck to you.. I wish I had some