Yes, a toothpick, cocktail stick or something like an unfolded paper clip is much better for applying paint to stone chips that the in-cap brush supplied in the Seat paint touch up pens, as you can apply the paint much more precisely to the damaged area.
Another option is to buy a Chipex kit. I’ve used these before and found the colour match to be good. They are quite expensive though and take a bit of practice to get good results. I found one of the big advantages of the Chipex kit was that if you made a mistake in applying the paint, you can remove it all with the supplied blending solution and start again. There are videos on the Chipex website and on YouTube showing
how to use the product.