Here is my product.wxs, how to install to two different directories.

<?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi";>
  <Product Id="*" UpgradeCode="C13B1269-945F-45C3-A80A-141A51E5BD02"
Version="10.0.0.0" Language="1033" Name="Xyz App" Manufacturer="Xyz Corp.">

    <Package InstallerVersion="300" Compressed="yes"/>
    <Media Id="1" Cabinet="myapplication.cab" EmbedCab="yes" />

    <!-- Step 1: Define the directory structure -->
    <Directory Id="TARGETDIR" Name="SourceDir">
      <Directory Id="ProgramFilesFolder">
        <Directory Id="APPLICATIONROOTDIRECTORY" Name="XyzApp"/>
      </Directory>
    </Directory>

    <!-- Step 2: Add files to your installer package -->
    <DirectoryRef Id="APPLICATIONROOTDIRECTORY">
      <Component Id="apple.exe" Guid="F8A6C429-F775-45EE-9DCF-28DA2839F2CC">
        <File Id="apple.exe" Source="MySrc\apple.exe" KeyPath="yes"
Checksum="yes"/>
      </Component>
      <Component Id="releaeNote.html"
Guid="A127ACBD-1F87-4D57-8E08-E0F8E5350510">
        <File Id="releaeNote.html" Source="MySrc\releaeNote.html"
KeyPath="yes"/>
      </Component>
    </DirectoryRef>

    <!-- Step 1a: Define the directory structure -->
      <Directory Id="SysFolder" Name="System32" >
        <Directory Id="SYSTEMDIRECTORY" Name="System32"/>
      </Directory>

    <!-- Step 2a: Add files to your installer package -->
    <DirectoryRef Id="SYSTEMDIRECTORY">
      <Component Id="myTest.dll"
Guid="098F3CB7-7A7D-4F7E-9042-49DF62C33694">
        <File Id="myTest.dll" Source="MySrcDll\myTest.dll" KeyPath="yes"
Checksum="yes"/>
      </Component>
      <Component Id="myTest.dll.sig"
Guid="098F3CB7-7A7D-4F7E-9042-49DF62C33694">
        <File Id="myTest.dll.sig" Source="MySrcDll\myTest.dll.sig"
KeyPath="yes" Checksum="yes"/>
      </Component>
      <Component Id="myTestNL.dll"
Guid="F2D689BE-CD57-4B86-8F90-485DBAC07721">
        <File Id="myTestNL.dll" Source="MySrcDll\myTestNL.dll" KeyPath="yes"
Checksum="yes"/>
      </Component>
      <Component Id="myTestUI.dll"
Guid="F2D689BE-CD57-4B86-8F90-485DBAC07721">
        <File Id="myTestUI.dll" Source="MySrcDll\myTestUI.dll" KeyPath="yes"
Checksum="yes"/>
      </Component>

    </DirectoryRef>

    <!-- Step 3: Tell WiX to install the files -->
    <Feature Id="MainApplication" Title="Main Application" Level="1">
      <ComponentRef Id="apple.exe" />
      <ComponentRef Id="releaeNote.html" />
    </Feature>

    <Feature Id="MainApplicationDll" Title="Main Application Dll "
Level="1">
      <ComponentRef Id="myTest.dll" />
      <ComponentRef Id="myTest.dll.sig" />
      <ComponentRef Id="myTestNL.dll" />
      <ComponentRef Id="myTestUI.dll" />
    </Feature>

  </Product>
</Wix>

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