Hello tawame -
TestStand can only load one StationGlobals.ini file at a time unfortunately, and there is no functionality in the software to automatically merge the two files. While this has been suggested for future versions of TestStand for right now you will have to pick one of the two files and keep it in the TestStand/Cfg folder.
--Regards,
Elaine R.
National Instruments
http://www.ni.com/ask