I am pretty OCD about keeping things neat. I think it has to start there for sure. I have seen lots of reloading bench pictures online, and some are neat as a pin, and other look like they got hit by a North Korean missile! For sure neatness has to start with the user. I clean up after EVERY session.
As mentioned, shelves and storage!!! No matter how much you think you need, it is never enough. Double it, and then double it AGAIN!!!