You'll need a post build JScript for your MSI file. Or you can do it manually in Orca.
var installer = WScript.CreateObject("WindowsInstaller.Installer");
var filespec = WScript.Arguments(0);
var msiOpenDatabaseModeTransact = 1;
var database = installer.OpenDatabase(filespec, msiOpenDatabaseModeTransact);
Execute("INSERT INTO `AppSearch` (`Property`, `Signature_`) VALUES ('SOMESOFTWAREVERSION', 'SomeSoftwareVersion')");
Execute("INSERT INTO `RegLocator` (`Signature_`, `Root`, `Key`, `Name`, `Type`) VALUES ('SomeSoftwareVersion', 2, 'SOFTWARE\\Some Manufacturer\\SomeSoftware', 'SomeSoftwareVersion', 2)");
Execute("INSERT INTO `LaunchCondition` (`Condition`, `Description`) VALUES ('SOMESOFTWAREVERSION <> \"#1\"', 'This application cannot be installed with SOMESOFTWARE v1. Setup now will exit.')");
function Execute(sql) {
view = database.OpenView(sql);
view.Execute();
view.Close();
}
It will check Wow6432Node on 64-bit Windows just as WiX does