I had to do a similar thing in my WiX project which builds both x86 and x64
MSIs.
Here is how I did some registry keys that needed to go both registry
sections on x64 sytsems.
<!-- 32-bit Registry Keys - Goes to 32-bit registry section
(WOW6432Node) on 64-bit systems -->
<Component Id="C_Registry_x86" Guid="PUT-GUID-HERE "
Directory="INSTALLLOCATION" Win64="no">
<RegistryKey Root="HKLM" Key="SOFTWARE\Acme\Product">
<RegistryValue Id="x86_Value" Type="string" Name="KeyName"
Value="KeyValue" />
</RegistryKey>
</Component>
<!-- 64-bit Registry Keys - Goes to standard registry on 64-bit systems,
cannot be included in 32-bit MSI -->
<?if $(var.Platform)=x64 ?>
<Component Id="C_Registry_x64" Guid="PUT-GUID-HERE"
Directory="INSTALLLOCATION" Win64="yes">
<RegistryKey Root="HKLM" Key="SOFTWARE\Acme\Product">
<RegistryValue Id="x64_Value" Type="string" Name="KeyName"
Value="KeyValue" />
</RegistryKey>
</Component>
<?endif ?>
Hope that helps.
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