An inverted bottle stops water flow, but does not when connected by a tube? I'm wondering why an inverted bottle doesn't overflow a container it fills once it reaches the opening, but when a tube is used then the water drains out completely causing the container to overflow and the bottle to become crushed/implode?

I think it has something to do with raising the height of the bottle, which increases the amount of pressure of the water going into the container.
Given this, is there a way to achieve maintaining the water level when the water bottle located much higher than the container?
 A: The tube system implodes the bottle because the height of the bottle above the lower reservoir determines the strength of the suction that develops inside the bottle. This follows from the laws of hydrostatics about which you can learn more on wikipedia. To prevent the bottle from imploding (and therefore draining out and overflowing the lower reservoir) at greater heights above the lower reservoir you need a more rigid bottle which can sustain more suction without collapse.
A: The column of water (the height of water) determines the pressure (and in this case the suction on the bottle too).
Since water is approximately incompressible, the pull of the extra pressure is transmitted to the bottle which is no longer able to resist the crushing force from the pressure differential of the exterior of the bottle vs the interior. The bottle getting crushed leaves less room for water inside it, leading the excess water out through the tube which is why the lower container overflows.
Two ways to maintain he water level are (1) increase the air pressure on the outside of the lower container (the air will apply a greater force on the water of the lower container and consequently push it into the tube and into the bottle), or (2) get a more rigid bottle and tube (since water is approximately incompressible, the suction of the bottle and tube will impede the water from flowing out).
