A couple of comments, since I read ProgrammerGeeks comments a little differently.
it did a search of my HD and built a libary, exactally what I didn't want it to do!
0. Thats pretty much the point of MC - you use the library to catalogue your media and sort out playlists, etc.
Do I have to import every sub directory directory seprate?
1. Importing (Tools, Import Media - set the base folder and choose advanced/search in subdirs) only builds your MC Media library, which points MC to the media files you wish to catalogue - it doesnt change any filenames/locations. You can view your library in a multitude of ways below Media Library in the tree in the left pane.
Under the section where it lets you browse by location on the side it only has the root directory with all my music this is not accruate to the drive
2. It sounds a little like you are looking at the 'My Computer' node in the tree, which functions a bit like Windows Explorer and will show you all media files. Its not the same as your library.
Also how can I get it to rescan all the files and update it's database.
3. File/Library/Update Library. Not the same as scanning your PC and importing all media files - see above. Might be best to backup your library first.
I have to use third party tools for renaming since this is uncapable of keeping my directory structure
4. MC will not rename your files, unless you select some files in the library and choose Tools/Library Tools/Rename files from properties. This gives you complete control for organising/renaming your files according to the file tags. Note the reverse Fill properties from filenames will tag well-organised and named files based on your directory structure and filenames.
it does to much
Well, yeah its pretty full-featured. You probably figured all the above out, but I sort of got the impression that some of what you were describing was not quite what Jim and King thought. Just ignore me if Im rambling...