Ok Solved it! Quick and dirty guide but will hopefully help.
The problem with this is its VERY skin specific. Most skins support smart playlists but only some allow you to configure the home screen as much as the one I'm using. The following screenshots are using the Aeon Nox skin (downloadable in appearance settings).
Step One:
TV Shows & Anime (or whatever) must be in different folders! - On my main setup I have them on different drives. D: for TV Shows, E: for Anime, F&G for Movies however for this I have a temp folder with 2 folders... 1 TV Shows and 1 Anime.
Add your shows to XBMC as normal, both as TV shows... once this has been done you will notice that all your shows combine with 'TV Shows' on the homepage.
2. Hit the .. to go up a folder to get into Playlists and
New Smart playlist...3. Select type as TV Shows, call it TV Shows (or whatever it is) and under Find Items Where you want to ADD
4. Select
Path and
Starts with - Important you change it from 'is' to 'starts with' ... that was the mistake I was doing
Type or Browse to the correct location.
5. Create a 2nd playlist for the Anime/Cartoons, point it to the correct folder etc.
6. Congrats you now have 2 smart playlists.
Now here is where it gets a bit confusing and this is where the skin specific stuff comes into play.
Go into Settings > Skin
Customizers > Main menu item customizer (backgrounds,widgets)
On the main bar scroll over to CUSTOM1 and hit Enter. When customising it you want to turn off Disabled, change type to Video Playlist, Choose the TV shows playlist, label it as TV Shows and Choose yourself a nice background.
Do the same with CUSTOM2 for your anime/cartoons.
DISABLE the default main TV shows otherwise you will have 2 TV Shows on your homepage (1 with everything, 1 with just TV shows)
Done! You now have 2 playlists on your homepage and your TV shows & Anime/Cartoons are separated!