He wrote down any interesting or potentially useful ideas on uniformly sized index cards on one side only.
Each new index card got a sequential number, starting at 1.
When a new source was added to that topic or something to supplement it, he would add new index cards with letters added to the number (1a, 1b, 1c, etc.)
These branching connections were marked in red as close as possible, where the branch began.
Any of these branches could also have their own branches. (For example 21/3d26g53)
As he read, he would create new cards, update or add comments to existing ones, create new branches from existing cards, or create new links between cards.