The Reds Vs Blues appears to be just a bit of fun, and to add a bit of excitement/competitive spirit to the show. The final ultimate winner - the person who wins the £250,000 opportunity to open/run their own restaurant - may be from either team.
The Reds Vs Blues is decided by customers comments and number of customers fed (something that each of the head chefs is trying to win for a bit of added kudos), whereas the overall winner is decided by the viewers votes