Well, you could always try Goof-Off on those areas and then re-stain those bits. Rubbing with a small soft brass-bristled brush helps to work it in. I really wouldn't worry about the bits that will be hidden and concentrate on any that show.

I have used coloured Sharpie pens to touch up the odd stain flaw, but it does depend on the finish used over the top, as some will cause the ink to separate. So best tried on some scrap wood first.