If you do indeed mount the reservoir bottle lower than the radiator cap, you absolutely must ensure that you do not have any air bubbles in the hose. I use a clear hose so that I can make sure that it is all coolant. When you install, put a small amount of coolant in the reservoir and fashion a way to hang it from the handlebars. Start the engine and let the coolant heat up until the rad cap opens and any air is expelled from the radiator. The air bubbles will vent out through the reservoir bottle. Stop the motor and monitor the level in the bottle to make sure that no air is sucked back into the line. Once cooled down you can complete the install.
If you do not do this procedure the coolant in the radiator will vent through the cap when it heats up and run into the reservoir bottle. However, the bubbles in the line will remain at the high point. As the engine cools, the first thing sucked back into the radiator is the air, not coolant. You end up with a fairly large air pocket in the top of the radiator thus minimizing its effectiveness.