To reset the cent offset back to 0 press both the up and down buttons at the same time. The tuner will store up to 31 custom stretches. The directions for how to do this are clearly outlined in the manual starting on page 24 with the flow charts. The instructions are clear as to how to use the tuner and by now you should be comfortable with the menus, selections and organization of the unit. My preference is to copy an existing stretch then merely adjust the cent offsets as you go through the tuning.
Most technicians stretch the upper octaves more than the lower ones.
You can skip over the lower octaves if you do not want to adjust them for now and finish the 5th octave on up. Then go back and edit this program after you have tuned the lower octaves aurally. It may be easier to tune the lower octaves aurally then measure those notes using the tuner to determine how much stretch you applied to those lower octaves. The tuner makes pitch raising much easier. I set the tuner to over-pull each section depending on how flat it is.