ANY changes made on the editor require you to start a new save game with the newly edited database to take effect, be it team colours or up to date transfers.
You can change you kits each season by adding new kits into the game, a guide on how to do so is
here
Regardless of what colour kits you put into the game, if they differ from the team's original colours the team colour bar will still be the original colours. ie Man United's away shirt in game is white so when using the away kit the team bar is white with black writing, if you were to add a blue away kit the white bar would still appear but in the club overview screen you will see a lovely blue kit.
Do not fear, as you can edit team colours in game using the Football manager real time editor(FMRTE) which can be downloaded
here make sure you backup your save game before making any changes with FMRTE.
To request a kit to be made for you how you want it then try
here make sure you follow the rules and be patient (its worth the wait)