Once you've picked what goes in, where you put it matters. Anthropic's guidance for long inputs (think 20,000 tokens and up) comes down to three habits.
Documents at the top, question at the bottom. Put the long material first, then your instructions and the question last. In Anthropic's tests, ending with the query improved answers by up to 30%, most of all with several complex documents.
Wrap each document in tags, with its metadata. A <document> holding a <source> (and any other metadata, such as a date) plus a <document_content>. Now Claude can tell where one file ends and the next begins, and can say which one it's quoting.
Ask for quotes first. Have Claude pull out the relevant lines before it answers. It has to find the evidence before reasoning from it, and you can check the quotes against the source.