Your question is far too 'open' to receive a single, comprehensive answer that won't mess things up for you.
Let's start off slowly....
Media Center will more than likely have all the tools you need to get your project done in good time, especially as you appear to have done the work setting the tags on your files.
Some of the library info may be saved in the files themselves, but all of your library info will be saved in your MC database.
When you use Media Center to move files around on or across your drives, Media Center will maintain all data relating to those files at the same time as moving them to their new location.
If you move the files externally, without Media Center's involvement, you are virtually guaranteed to experience a certain ammount of irretrievable library data loss.
All of the above is especially important with regards to video files, where, depending on the file type, the file will contain no tag info at all. MC14 goes some way to addressing this issue with the introduction of .xml 'sidecar' files that hold the tag info of all such video files.
My suggestion for you right now is to copy some of your files into a temporary directory and import those files into Media Center.
Create a smartlist (Press F9) and create a rule that lists only those files you copied. For example, if you copy the test files to a directory at "D:\Test Files" then the following rule will ensure that only files that are in that folder, or its sub-folders, will show in the list: [filename (path)]="Test Files"
Having done that, select a file or two in this list, right click on your selection, hover over "Library tools" then click on "Rename, Move and Copy Files"
Play with this tool for a bit and see what happens to your test files. You should quickly see the power that is available to you.
If you get into a "whoa, that's not what I wanted" scenario, pressing ctrl+z will undo whatever you just did.
If you use the tool to move your test files outside the "Test Files" folder, they will be removed from your list (as they will no longer match the rule) so when experimenting, try to keep Test Files in any file path you play around with.
Having familiarised yourself with this tool, if you have any other questions, just shoot, answers are never far away.
When asking, try to be specific about what you have currently, and where you're trying to get to.
Finally, when you're done learning and ready to work on your real files, remember to delete your test files, otherwise, the duplicates in your library will drive you nuts!!
Have fun,
-marko.