For efficiency, you would want to use a switching regulator for both routes. The 'down' switcher, removed the need for the inductor, but remember that you would only be able to discharge the batteries to just over 1.25v, before you lose the ability to deliver 5v, which will give less utilisation of the available power in the cells. Realistically, the boost regulator, done with an IC, designed to do this, should quite easily get over 90% efficiency, and use ost of the available power in the cells as well. However remember that board design round a switching regulator, needs to be carefully done... The battery in the last Ipod Ilooked at, was only a 150mAHr cell, and this was quoted to give 3 hours typical life (giving a consumption of perhaps only perhaps 50mA to 60mA - given the extra losses at the '3 hour' rate, versus the power normally quoted at the '10 hour' rate). The circuitry drew about 400mA, _when charging_ the battery.
Best Wishes