DisplayFusion should work fine via Remote Desktop. I've tested with RDP sessions using two and three monitors and haven't had any issues.

As for the machines with four monitors, if there is a Window Location rule setup for an application to open on monitor 3 or 4, but you've only connected using two monitors, the app should just open on monitor 1 or 2. I tested this by connecting to a machine with three monitors using a machine with only one monitor.

If you'd like to give it a try before purchasing, you can get a 30-day DisplayFusion Pro trial key here: http://www.displayfusion.com/Trial/

Please let me know if you have any other questions.

Thanks!