This technique applies whether you have just finished your repair, or you have an area of factory painted finish that you want to apply color over. In both cases, you can apply base color over the clear coat, however you have to prepare the surface first. 

1. Let the freshly painted clear coat fully cure by waiting a couple days. If you are painting over a factory finish, this doesn't apply.

2. Scuff the surface with a 1000 or 1500 grit sandpaper, ideally by wet sanding. This promotes adhesion of the base color.

3. Wash and degrease/wipe down the area with a prep wipe.

4. Apply the base color as you normally would, typically 3-4 thin coats to achieve coverage and color match.

5. Clear coat the new repair as you normally would.