The root file is a realisation of the logical design of a document. It should therefore be complete when first entered, although the % character might need to be used to comment out most of the \include commands. By doing this, you ensure that none of the items in your plan get omitted by accident. (An alternative, and maybe better scheme, is to create the chapter and section files too, and to provide short summaries of intentions in the section files. This way, all of the document files are created at the start, although most will only have interim contents.)
is a large and relatively slow program. Dissertations are typically quite large documents, and so we need a means of reducing the time spent processing text which is essentially fixed and completed. This is particularly important as the document increases in size. The mechanism for doing this is provided by the \includeonly command. This directs to only process those \include entities that are listed in its argument. In doing this, will still read the .aux files for the omitted entities, in order to get page numbering and cross-reference information, but it will not process the textual parts. This generally speeds up processing very significantly.
(Note: If you use the \includeonly facility, and have organised the page numbering so that you switch back to arabic numbers at the beginning of the first chapter, you need to keep this chapter in the \includeonly list to avoid odd effects with page numbers!)