The reason you feel it's a bit messy might be because MC have gotten some meta data wrong? Use standard view with panes (media sub type, tv show and season is good). Then you can check that every TV Show and Movie are tagged correctly and are placed together. If something fails consistently it would be good to give the file names here, and it's possible that the automatic lookup system can be adapted. After you have made sure they are tagged correctly, you'll want to test out some view. You can create your own, or use the default. Also make sure you test out Theater View, which is my favorite (ctrl + 4). you can also change and add these views as you please.
As for keeping the content of your directories intact and use that data, you might want to ensure that you import the data without the automatic lookup enabled. And then see if MC detects your images and such on it's own. If it does not, there are probably some differences in the accepted name and placement of the files you want. MC will however give you most of the art work and meta data if you use the automatic meta data scraping system, but it's up to use if you want to use it or not.
Also have in mind that this program often takes a bit of time getting used to. But once you know how it can be done, you can almost do anything. Have a good look at all the options and then try to create some views in standard view and theater view would be my suggestion.
And by the way. It's called Media Center 17. Not Player
