I know this question is old but for those looking for a super quick and dirty way with C# to do this, and not use C++ or C:
Registry:
Modify HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution Options\magnify.exe (Add it if you need to) and then add a String value to the key:
Debugger
Make Debugger value equal to the path to the exe you want to run. Just tested this solution with a C# application on Windows 7 and 10 and both work as expected (You must launch the Magnifier with Win+U, or use Easy of access center.
Here is the output of my registry for this key:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution Options\magnify.exe]
"Debugger"="C:\\Path\\to\\exe\\application.exe"