Build configuration with multiple VCS Roots combines them into one directory

I'm setting up a build configuration for a Visual Studio solution that contains projects from 2 different GIT repositories.  In my local environment it's like

- project1
  - src
    - project1.sln
    - Service
      - Service.csproj
    - Web1
- project2
  - src
    - project2.sln
    - Web2

In the project2.sln, it uses the Service.csproj from from project1.


However, with TeamCity, when I setup multiple roots it comingles the contents of each repository into 1 working directory.  

- build
  - src
    - project1.sln
    - project2.sln
    - Service
      - Service.csproj
    - Web1

    - Web2

Is it possible to maintain their sibling structure in TeamCity like it is on my dev machine?  Or would a submodule be better for this?