I know its two different exam boards but does that mean people doing Edexcel gcse papers will have a different paper to AQA?
Yes. When I changed school's for sixth form, the whole year had done different GCSE papers to me, which did get quite annoying when the teachers would say 'so, you remember when you did this at GCSE?' and they'd simply assumed everyone had when I hadn't.
The papers are different for Edexcel and AQA since they are different exam boards. Sometimes, different topics (within the syllabus though) come up on the papers but it really depends on the exam paper style, topics chosen by examiners, etc.