I am horrible at this! I write maybe a hundred pages, out of sequence, on one long text document. Then have to organize them later...
To stop myself going mad I now try and use a numbering system, a very simple one.
If I am writing on a word document number the first page 1. second page 2, third 3 and so on. Then when you know you want to link a page literally write at the bottom link to pages 4 and 7. Then write 4 and 7. This way at least there is a traceable way to follow it through.
Other suggestions might help more though since as I said, I am terrible at this.