In regards to your first couple of questions here is the sequence of events I use to enter in data for a long range shot.
1. Enter in base line data like date, location, time, rifle, ammunition used, environmental conditions, target size, etc...
2. Knowing the distance to the target enter the base line elevation setting taken from your dope chart or ballistic app, same goes for the wind setting. Lets say I'm shooting at 600 I'm going to put in something like 4.2 mils and .5 left wind.
3. Take your first shot and note the impact on target. In the data book enter the call of the shot(where the crosshairs were when the shot broke).
4. Make any necessary corrections and note that in the next shot column. Say I was a little low and on the left edge of the target so I dialed in 0.2 mil more of elevation and shaved 0.2 mil off my left wind hold. In the #2 shot column I'd enter in 4.4 mils for elevation and .3 mil for my wind hold.
5. While I'm doing this I'm also marking my shots on the target diagram located on the page.
I pretty much do this until I'm satisfied that I have sufficient data at that range and want to move on to the next. The bottom of most data book pages also has a section for notes such as your shooting position, something that might have changed in the conditions, etc...
To answer your last question there are specific pages that can be used when zeroing at 100 yards but they are pretty much just like the pages you would use at longer range except they have typical zero target diagrams on them (circles, squares, etc...).
Hope that helps.