I have a few chips in my paint that shows bare metal.

I got some of the touch-up paint from a Toyota dealership and they said this is all I needed.

I started reading the directions after I got home and it says to apply it in one direction and to wait 30 min before each coat (easy enough). After 24 hours, apply clear coat. I didn't get any clear coat and I am not sure where to get the stuff.

 

You can get clearcoat at any auto store or even wal-mart.

If it's showing bare metal though, you should get primer touch-up.

 

I believe the clear is supposed to be mixed into the paint pen you got from Toyota. It should be fine though, my touch up spots on my 2ES are still good and its been years

 

Yeah it is showing metal and the start of some rust.