Create a GPTS Expert! How to train GPTS?

I am creating a tool that analyzes and critiques text files uploaded by users based on the knowledge (papers, books) provided to GPTS in advance, but when I upload the file I want to analyze, gpts reads and analyzes the knowledge I provided in advance, or when it analyzes it, it gives an ambiguous answer about whether it read the uploaded PDF correctly.
Does anyone know of any instructions that clearly distinguish between the uploaded file and the knowledge provided in advance?