For people just trying science or math notebooks for the first time my main advice is to do what works best for you, within the guidelines of making the notebooks student centered. Everyone has to find the best set up, meaning types of notebooks, what you want in them, and how they are used, that will work for your needs. Notebooks are not stagnant, so if the actual notebooks doesn't work this year, change it up next year.
I keep notes in my notebook as the year goes on, I make these notes bright and flashy so I can see them later, these notes are things that work and don't work for me and/or my students. If you are just starting and don't know what you really want your students to put into your notebooks, some suggestions. First, read some articles and books about the components of a notebook. There are some helpful websites and articles on my Live Binder about the various components of a science notebook. (I'm still working on my math notebook ideas). Make a list of the components you want your students to have in their notebook.
Once you have an idea of the components of a notebook, lay out a notebook. Take one of your lessons that you know you'll be using this year. Lay it out in the fashion, just like your students would do, and make it fit the lesson. See how it feels and works for you. Change it if you feel necessary until you have a working feel of what your notebook is going to be like.
Next dive in with your students!!! You'll know what works and doesn't work for your students and it's okay to change your notebook components as the year goes on. The important thing is to model for your students what you want, your exceptions, and give them time to work with their notebooks. Look at them often and give them time. My students have not used science notebooks when they enter my class at the beginning of the year, maybe in first grade, but that was awhile ago and in a different format. I do spend a lot of time early on helping my students work through their notebooks, but in the end, this time pays for itself and my students become very independent in using their notebooks!