The problem with your heater lines being higher than the top tank of the radiator can be cured by putting in an air bleed valve near the fire wall in your outlet hose,,,you can use this to bleed air from the cooling system,,,,also,,,if you install two screw capped tee's,,,one on each of the heater lines(near the fire wall) you can begin by putting your antifreez full strength into your radiator,,,then put a garden hose on one of the heater line tee's and open the other tee,,,,then fill slowly,,,this will insure that you are filling from the highest point,,,and you won't get big air pockets in your cooling system,,,,,just shut the water off when you see coolant(antifreez) coming out of the other heater line TEE.
As to your question about the overflow bucket giving back it's coolant to the radiator,,,,,,think of it this way,,,,,as the coolant heats up,,,it expands,,,,and as it cools,,it contracts,,,,so in a sealed system,,,,as your engine cools down, the water as it cools in your system will create vaccume,,and pull the coolant back from the overflow tank.