In terms of your description to the question, there are a few ways in which you can create themes, codes, sub-codes from different nodes, and you can also use NVIVO to link more than word frequencies. To get a grip on this, I would suggest familiarizing yourself with the following free training materials on YouTube:
Hi Peter - there are many different ways to create a codebook, but after exploring the data in NVivo, a general structure would be the following:
1) Research Questions
2) Coding Protocol (e.g., provide detail on how you will code responses, such as if the entire response will be coded or only the key words; also explain how many levels of coding there will be - 1st order, 2nd order, etc.)
3) 1st Order Codes (and their descriptions)
4) 2nd Order Codes (if applicable, and their descriptions; these are subgroups under the first order codes).
Feel free to check out the supplementary material for one of my papers, which has an example of a codebook on page 32.
I recommend that you read through your codebook many times and update the codes so that they are consistent and applicable to your data. It's also important to share the codebook and a percentage of your data with other researchers/coauthors (e.g., at least 5-10 percent) so you can check for coding consistency (e.g., percentage overlap), and then make any necessary revisions to your codes and codebook.