It's handy to have extra bottles around to switch up flavors. You can just rinse them with hot water, unless it was a stubborn flavor like cinnamon or something.
The tubing in my old Reo I always just used a syringe and flushed it out with hot water multiple times. Sometimes I would fill up the bottle with hot water and then squeeze it to run the water
through the other way too. Then just use a paper towel to clean off the top and then blow
through the top to get the rest of the water out of the tubing. It's a good idea every so often to take out that little o-ring in the cap and rinse it off...be warned though, it's a PITA to get back in there. And even more a PITA to get the cap back on the tube.