Well, I've done it a few times and its not that hard. The hardest part for me was "am I doing the right thing by putting sand paper to a brand new vechicle". I learned by doing it to friends and co workers cars first. I would tell them I'm not sure how it will come out, and they trusted me and were going to have a body shop paint the parts before I spoke to them. After I did the work, none of them went to a body shop.
There are a few different steps I've tried. All depends on the issue. From what you explained, this is how I would repair it. Always work in an area that is clean!
1) Make sure you have enough paint on the brush, but not too much where it wants to drip off the brush.
2) Fill in the scratch with more than what you need.
3) Use a rubber glove to remove excess, Ive also used a credit card as a squegee.
A) I have also left the excess there and sanded it down.
4) Let the paint dry. I like to let it dry for 24 hours. Drying times vary on weather and how humid it is.
5) Now that your paint is dry use the scratch-X to polish the area and clean off any paint that was smeared during the filling process.
(From how you explained your scratch, the paint should have dried / settled. Meaning that your scratch should be filled with your base coat / color, you know have to make the decision if you need to fill it one more time to level it out again (it should be slightly lower)or apply your clear coat)
The process is easy, just take your time, and try to use the scratch-x first before the sand paper. I've used model car sand paper. Its the perfect size for a repair, and ranges from 3200, 3600, 4000, 6000, 8000, and 12000 grit.