Very vague description of you project 
I would develop the sketch on a "normal" UNO while trying to reduce code size and RAM usage. It is much easier to debug if you have a serial connection.
I don't think it makes a difference if you optimize your code for speed. Running 1 or 100 milliseconds once an hour is irrelevant to power consumption. Your batteries will self-discharge much earlier. See also Nick Gammons excellent power page