Teams automatically switch sides each round in every gametype except infection. In fact there is no way to turn off the side switching which has created problems for some people.
Uhhh... there are no "sides" in KOTH. Both teams fight over a neutral hill. Perhaps you're confusing KOTH with Territories.
Sorry I meant to say there is no way to turn it off and accidentally added a w to the end of no. There shouldn't be any reason it would be a problem for your map. It was meant to balance games on asymmetrical maps.