paint. They can be buffed out by hand with any of a number of very, very fine scratch and swirl removers. (I detail cars as a hobby).
A great source for information is here:
http://www.autopia.org/The folks there can give you tons of tips on how to remove those fine scratches. If the paint isn't chipped,you don't need touch up paint. There are very few fine scratches that can't be buffed out with a little effort and no harm to the finish.
As far as product recommendations go, you could pick up some Meguiars Scratch-X at any auto parts store and that will take the scratches out, simply put a good wax job on the car afterwards because this stuff will remove any old wax. My personal choice though is to use Poor Boy's professional products
http://www.poorboysworld.com/ Low priced, and they do the job wonderfully. Their SSR line of products will do the trick for you, I almost guaranty it.
Now, on those stone chips and such, I recommend using the touch up paint you have, but in connection with this kit from Langka
http://www.autogeek.net/langka-paint-chip-repair-kit.html Basically, with this kit, you fill in your chip with your touch-up paint until it is a bit higher than the level of your existing paint, then you use the chemicals included in this kit to remove the excess. It works VERY well.
If you have any questions, PM me, I'll be glad to help.