The way to do this is quite simple, but you will have to edit the Visual Studio Project (csproj or vbproj) file in a text editor. See this MSDN blog post.
Here is the relevant XML snippet:
<ItemGroup>
<EmbeddedResource Include="bar.resx">
<LogicalName>notfoo.bar.resources</LogicalName>
</EmbeddedResource>
</ItemGroup>