I haven't printed anything up in landscape yet but I would imagine that if the layout of the PDO file is landscape then you would want to select landscape on the Cameo Controller too. Worst case scenario is that it will cut out your patterns upside down and then you will have your answer and will just have to reprint that one page. So give it a shot and see what happens.
Thanks for all your help Darkside, it's greatly appreciated, I'll give it all a shot when I get home. And from now on I'm going to make sure everything is printed Portrait view, haha.
Just wanted to say I made a portrait facing file and tried it when I got home, after just a bit if playing around getting my distance between the registration marks right, I got it to cut damn near perfect. Slight shifting here or there, but basically talking about on one side of the line versus being on the line itself. So thanks very much Darkside!