The reason for having it low is two fold, First heat rises, forcing the cooler more dense air downwards... towards your feet. Your torso will be nice and toasty but your legs and feet will cold.
Secondly, the higher you mount the heater core the harder time the water pump is going to have pushing the coolant through it. Depending on your w/p output you might have to put a booster pump inline with the heater hoses to circulate more coolant through the core. That's why i would have to suggest keeping the heater low down and the hoses as short as possible. More circulation more heat.