By default komoot will place your waypoints closest to the current route, no matter which order you added them to your Tour. If you want your waypoints to appear one after the other, in the order you add them to the Tour, you can do this the moment you place them, if you select "One way" instead of "Round trip".
Add your start A and the first way point as an end point B first. Then click on the map to place your next way point and choose "Set as new end point". You can also hold down the alt key on a Windows computer (option key on a Mac) and click on the next point along your route. On the spot you chose, a new waypoint will appear, which will automatically be the new end point of your Tour.
Add your start A and the first way point as an end point B first. Then tap on the map to mark your next waypoint and choose "Set as new end point" on Android devices. On iOS devices, you need to tap on “More options” first and then select “Set as new end point.”