I find the shame about this question is that It's all comicbook physics you are asking about, there IS no real answer. And yet ever Since Alan Moore and his 'Anatomy Lesson' comicbook writers, and to a lesser extent the fans, have been reprogrammed into thinking everything has to be explained about these characters. They have to be completely plausible and make sense.
In the pre-Speedforce days they were both characters who just had Superspeed, they could run fast because they could. After the Speedforce it was much more the case that The Flash's connection to it was so intimate that he would always be faster than any non-speedforce user as he was drawing on a universal and primal form of energy. Out os all the other speedsters he was top dog as his connection to it was the strongest. When Wally became the Flash he was limited to 710mph, gradually improving to be Supersonic. As the logic of Mark Waid had it this low leel of speed was almost certainly because he was not tapping the Speedforce, a fact reaffirmed at the end of Infinite Crisis when the Force dissapears and Jay Garrick is left at... just 710mph.
So going by the logic Mark Waid introduced and which was adopted by his successors The Flash is the Fastest Man Alive because he taps the almighty Speedforce, take that away and... there wouldn't be much left to him.
Superman on the other hand is powered by the Sun and his body processes that power to enhance all his physical traits, even his super intelligence in some canons. So his personal speed is logically due to his muscles being supercharged and tied into his physical stamina.
So If Wally/Barry is drawing from the speedforce it becomes a question not so much who is faster in a race, but who has the better stamina. Does The Flash have better stamina than Superman...? Should he?
Superman has been shown to be able to fly as fast as barry can run though, and as long as he has access to solar energies, both can go on long time?