Home depot, lowes and even walmat carry the guardsman stain pens. Their made to touch up furniture and you can layer them for the desired color. They come 3 in a pack in different shades of brown. Works very well, but as with most stains, they can smear if the sealer/finish re-activates them. No matter what you use, Test on a scrap piece first with sealer and finish waiting the normal times. I would give atleast 24 hr dry time just on the stain itself.
Hope this helps,
Dave.