The manual is written to cover all three LEAF models so some of it doesn't apply to the S model. The charge timers for the SV/SL are covered in the part of the manual called "With the navigation system". For the S model you need to look at the part labeled "Without navigation system", page CH-24 in the 2014 manual. Yes, they could have made that clearer.
The S model has only one charge timer and it is set by the dash buttons. It is End-time only, there is no start-time setting and no days of the week (it is the same for every day of the week). Set the time you plan to leave home and the timer will have the car charged by then. Since it finishes charging somewhat early, you might want to set it for a bit after you plan to leave, especially if you want a charge of less than "100%" (so that you have some regen braking, for example). Make sure that you have your AM and PM right (or use 24 hour time). And make sure that you set the timer to "On" (page CH-25)! You can turn the timer on or off without changing the timer setting, if you wish.
The climate control timer works the same way as the charge timer (and is different from the SV/SL models that use the nav system for timers). On the S model the manual (page 4-12 to 4-14) says that the CC timer setting is for when the climate control system "starts to operate". I think that is a mistake and that the time you set is when the CC system is supposed to be ready (heated or cooled), i.e, "end-time", just like the charge timer. Since I don't have the S model I can't verify this; you will need to do the experiment yourself or hear about it from someone else with an S model. However it works, you would use the dash buttons to set the time just as you do with the charging timer. You can then turn the CC timer on or off depending on whether you need it or not. Please be aware that the CC timer works only when the car is plugged-in.
Hope that helps.
10-31-15: 30,800 miles, Battery Capacity: 55.52 Ah [from LeafDD] 227 Gids at 100%
Lost first CB 6-3-15, 55.75 Ahr, 26,939 miles
Blue 2012 SV ordered 8-30-11 (Colvin Auto Ctr, McMinnville, OR), Delivered: 12-15-11