Format Document

I need to fix around 12 documents totalling around 144 pages.
I need to fix table of content, header and footer, page numbering. Also, I need to combine all documents into one but at the same back I need all the documents back separate to work on them separately in the future.
I want to be able to see all the subthemes at the left of the documents to quickly go to them.

There is one thing that I hope you will understand, all the documents are in spanish. I already have all the contents, I just need to make it look good and in good format.