Up to you, both approaches are valid. I think if you have a lot of explaining to do then perhaps a LoE within each section rather than a 50 page LoE may be better. But if you can fit all your explaining in a short and concise letter, then just upload it in the correct place holder.
Thanks for the answer. I don't have lots of explanation but I thought it would be better to have an letter of explanation with the other documents for each section so it stays together.