I would say tick the “keep itunes folder organised” box, it does it really well, and is well organised.
If your music isn’t tagged, then tag it, actually spending a bit of time getting everything sorted in the first few weeks of using itunes just makes the whole experience nicer in the long run. Adding the correct genres ect to all your music, makes play lists and listening options so much more expansive.
And If you have music ripped from cd’s into mp3’s, I would suggest ripping them again into apple lossless format, larger file size but better quality. If you don’t want to redo your old stuff, at least do future rips in that format (I don’t think it converts files imported from other folders, just when ripping cd’s).