Is the Arduino the SMPS controller? if so you will have to measure the peak current when the switch is on and compensate for the inductor current by averaging several 'cycles' and controlling the pulse width from that feedback.
The alternative that I like better is to use a CC supply for each Led (they are available for less than $5.00 on Ebay) and monitor the current drawn by the CC supply for current and time used to make a 'gas gauge'.. instead. You could give your sketch the AH capacity of the battery used and when 40% is gone indicate that this is the 'half way' point so that either reserves can be added or turn around and go back.
While it is entirely possible to use the Arduino for both... it is of questionable utility as it has been pointed out that Freescale has been at this for some time.
Sometimes the Kiss method is best.
Bob
{Edit RKJ}