A few things:
1. Separate each part of a document into different TeX files and include them in the main document. Each file should be a separate unit of the work. Only compile the main document when you need to.
2. Generally write with readability in mind and use newlines and other whitespace in the source a lot more than you think you should.
3. If you have common boilerplate that you frequently use at the top of docs, make your own package(s) for those commands and maintain that separately.
4. Refs and labels everywhere you possibly can. Also, prefixing your label names helps a lot, so \label{clouds} on a picture of clouds becomes \label{fig:clouds}. If you are writing a book, and this is the chapter on the sky, consider \label{fig:sky:clouds}.