With a library that size, if you like your on-disk organization to be a very specific way, and you want to move files and folders around, I can totally understand.
So, with that in mind, you should learn to use the Rename, Move, and Copy files tool. Don't do it through the Mac Finder. Do it with RM&C.
http://wiki.jriver.com/index.php/Rename,_Move,_and_Copy_FilesI do about 95% of my moves and renames with RM&C. This includes audio as well as video files. It's very powerful and easy to use once you understand it. At first it seems a little complex. But once you get past that, it's a really fantastic tool. It's really one of MC's best features that doesn't get a lot of attention.
Sometimes I do moves outside of MC. In those cases I generally do something that's simple and I still use RM&C to UPDATE MC's database, so it knows where my files have moved to. I do NOT want MC re-importing my files as I move them. I want MC to keep the same information about all of the files, all the time, even when I move them. If you move externally, and re-import, MC may lose some information and re-write things like the Import Date.
So learn to use RM&C and be happy.
Brian.