You can eat energy gels at any time. 1 gel gives you 1 extra km for that turn. (it costs you a little in terms of health damage though)
You can use up to 2 hours worth of time. So if you rest for 1 hour, the other hour does't get used.
This was more useful when i had it set up so you could rest AND run in a single turn. But I've stopped doing that because it just gets really confusing really fast when I do the calculations.
So if you're going to rest it would make sense to rest for 2 hours ;-)
Ok. Thank you for making this clear :D I didn't get this from the instructions. About the gels, this means I can't really use gels if I am only resting, right?