If you are loading up your own personal videos, it won't much matter how you store it but will impact how you can display it. If you're planning on digitised films, TV shows etc, then not complying with sructure requirements negatively impacts the ability of Emby to 'scrape' databases (IMDB, TVDB and so on) to fill in metadata for you and build cast prgiles, director details, episode lists, descriptions etc. Now you
could, of course, do most of that manually and for home/personal videos you'll (obviously) have to, but for a large collection of flms and TV progs it's either going to take you a very, VERY long time and shedloads of work, or you wanna get the folder structures such that they comply with what IMDB / TVDB et.al. expect.
Which brings me to my main criticism of Emby. The sftware,
IMHO, is damn good. The documentaion .... a bit less so. I mean, most stuff you need is there, but it shows signs of being written by someone that already knows how the software works, and not used in anger by someone trying to work out how the bleep to do this, or that. That bit me, a little. I got there, by careful reading and expeimentation. But instructions are not always cler or comprehensive, and a bit stingy with examples.