Ok, first of all, clear can not be mixed inside of paint. Chemically, the paint dries with gloss...this is called "single stage" paint. Most likely it is Lacquer that you got from Honda or maybe even Enamel.
Second, if you were sanding the scratch down you would never use a touch-up brush with paint...if you sanded, the paint must be sprayed on...otherwise you will see the repair like a sore thumb.
Thirdly, If you sanded and can still see or feel the scratch then you did not sand enough. You should be able to run your hand along the area with your eyes closed and not be able to tell there was ever a scratch there.
Lastly, what grit sandpaper you used will determine if scratches can be buffed out....in your case a would not try to buff it out.
My advice to you would be to sand the area smooth with 600-1000 grit sandpaper and spray paint it. You can get custom matched cans of paint using the color code off your car which is located in the driver's side door jamb, near the lock pillar....its a white sticker and will look something like this: R81P-3 or YR583M-4 or NH734P.
with that color code you can go to
www.paintworldinc.com or call 1-800-548-4321 and get spray paint for your car delivered to your door in a couple days.... their inexpensive, and I've used them for years.