Our Monitor Profiles feature enables all of the monitors at the same time, instead of how Windows does it where you have to enable one, apply, then enable the next, and apply again. Unfortunately this might cause the desktop icons to get jumbled up.
The good news is the DisplayFusion 4.0 Beta versions have a Desktop Icon Profiles feature that allows you to save and load your desktop icon layouts. The final version of DisplayFusion 4.0 should be available soon, but if you'd like to try the Beta in the meantime, you can grab it here: http://www.displayfusion.com/Download/Beta/
At the moment, the Desktop Icon Profiles have to be loaded manually by selecting them from the context menu, or by setting up a HotKey for the profile. In the future, we're planning to add the capability to assign a Desktop Icon Profile to a Monitor Profile, so that it will be automatically applied.
Hope that helps! Please let me know if you have any other questions.