Locke here describes a method of laying out a commonplace book so that the index requires only a fixed amount of space, and pages are not wasted. He assigns to each topic a keyword, and places the entry in a section indexed by the first letter and first (following) vowel of that keyword. When more pages are needed for a given two-letter index key, he finds the next blank page, and records a two-way link between it and the former, and continues.
This method provides only a very minimal degree of indexing–you must check every page listed for a given two-letter combination, in order to find a particular entry. Its primary virtue is saving paper.
I have adopted the system of writing forward and backward page references to connect items in my own reading notes; it's much better than trying to guess how much room I'll need, and I certainly cannot refrain from reading a new book while another is in progress.
I have not adopted the indexing system. Instead, I record the pages on which my notes appear on the book's catalogue card or in its electronic entry. There's no need to resort to inferior pre-computer systems merely for the sake of consistency!