If you have any paint left over from you re-paint, use it. If you had a shop do the paint job, go back and see if they have any of YOUR paint left over they will give you. Even if you have the paint code for your color, there will still be some minor color differences between mixes...
As far as the touchup goes, I like to use a q-tip dipped in the base color to GENTLY fill in the chips. As long as the chip is not all the way through the primer to bare metal, you should be fine. I usually don't worry about clear coat on small chips because it is very hard to smooth it to match the rest of the paint job.
When you are test fitting parts and assembling, I like to use tape on all the edges to help mitigate scratches and chips. This works especially well on putting fenders and doors on.
Good luck and don't stress too much on the chips. They just let people know you actually drive the car!