There is a video here which provides you options about the Window Layout Wizard.
https://www.youtube.com/watch?feature=p ... A3MqP6LAAgIn the Windows Layout Wizard, on the right there are a few options you can set. One of those options is "Use Monitors". You can click on the ... (ellipses) button and in the popup you can re-order the displays, or even remove them from consideration of location of the regions.
I've found the right timecode in the video for this option description here.
https://www.youtube.com/watch?feature=p ... LAAg#t=348For creating Layouts manually, the easiest way is usually to create a layout using the wizard which is close enough, and then modifying it. There isn't really any written guide I can locate on creating manual layouts, despite that many people do them. TBH, they aren't too tricky when it comes down to it. The video above provides you all the info you need to know, and the options that are in the wizard are pretty much the same as those in the manual layout, but the Wizard does prevent you from breaking it. ISBoxer does tend to prevent you from exporting your profile if there is something wrong with the Window Layout (although it doesn't pick up every single issue), and the error message is usually understandable as to any issues. Failing that, there is always this forum or the irc channel.