Atherton was far less successful in First-Class cricket before his Test career than during. For Lancs he averaged 36 1987-1989; 1990-2001 he averaged a full 10 runs higher, 46. However hard he found it to motivate himself, make no mistake, he managed it.
Vaughan averaged 37 for Yorkshire 1994-1998, which is a pretty damn decent effort for a youngster who plays half his games on the most seaming deck in the country. Vaughan gets all the "they looked beyond the county averages" because a) he was picked in 1999 after a very poor season and b) he'd done absolutely dreadfully for England A which pulled his career First-Class average down. Vaughan then averaged 50+ from 2000-2003, which encompassed most of his success at Test level. He then averaged 25 2004-2009, when he mostly just popped-up in the occasional game without having the chance to find his touch, and was often trying to play when unfit (to prove his fitness) to boot.
Vaughan was, by-and-large, a reasonably successful batsman at county level, and by-and-large a considerable disappointment at Test level. I'll leave my thoughts about Trescothick aside for here but suffice to say I never rated him as a Test batsman above Graeme Wood or Andrew Hilditch.