WiX supports creating a 64 bit MSI, however you have to alter the csproj file for WiX if you are using the WiX projects created by the WiX toolset. Where normal projects would let you open properties and set the Platform, the WiX projects do not, through the GUI anyways.
Below will allow the project to compile in x64 (I don't support x86, so I don't setup both).
<Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
<Platform Condition=" '$(Platform)' == '' ">x64</Platform>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x64' ">
<OutputPath>bin\$(Configuration)\</OutputPath>
<IntermediateOutputPath>obj\$(Configuration)\</IntermediateOutputPath>
<DefineConstants>Debug</DefineConstants>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|x64' ">
<OutputPath>bin\$(Configuration)\</OutputPath>
<IntermediateOutputPath>obj\$(Configuration)\</IntermediateOutputPath>
</PropertyGroup>