You still could split client and server in two repos, and keep the same folder structure for the developers, since both repos could be declared as submodules in the parent repo.
And you can setup those submodules in the parent repo in order to follow the latest commits of their respective master
branch.
That way, it is easier for TeamCity to follow only the commits of one specific repo (the client on, or the server one), since partial cloning isn't supported with git.