Let's say you have the DLLs build for both platforms, and they are in the following location:
C:\whatever\x86\whatever.dll
C:\whatever\x64\whatever.dll
You simply need to edit your .csproj file from this:
<HintPath>C:\whatever\x86\whatever.dll</HintPath>
To this:
<HintPath>C:\whatever\$(Platform)\whatever.dll</HintPath>
You should then be able to build your project targeting both platforms, and MSBuild will look in the correct directory for the chosen platform.