This can be controlled by keeping both masthead files under some directory and depending on the server selected just move the masthead file to the installer location. Directory structure would be like this:
./setup.exe
./mastheads/server1.afxm
./mastheads/server2.afxm
./installClient.vbs
installClient.vbs will accept the name of the bigfix server and will move appropriate masthead file to upper level directory so if you run the vbscript like this:
cscript installClient.vbs server1 then directory structure will change to following: