It depends on the flavor. Some flavors, like cinnamon or menthol have a lot of staying power, in fact a lot of people will dedicate one atty to that flavor. As far at the cart and filler, usually hot soapy water then a warm water rinse will clear out most flavors.
Your atty cleaning method could make a difference too. Check the attomizer forum for a lot of suggestions on different methods. Personally I rarely clean my attys, just let them drain at night and blow them out when they start getting a little clogged. When I do clean, I either use hot water or PGA, let them soak for a little bit, then blow them out. Let them dry overnight and put them back into use.
I think the best overall solution is to have multiple attys each dedicated to specific flavors or flavor types.