Configuring MVC 5 project with service layer and DI and UOW
public class BaseController : Controller
{
    protected IUnitOfWorkService UnitOfWorkService;
    private readonly IEmployeeService _employeeService;

    protected BaseController(IUnitOfWorkService unitOfWorkService)
    {
        UnitOfWorkService = unitOfWorkService;
        _employeeService = unitOfWorkService.EmployeeService;
    }
}
public class HomeController : BaseController
{
    private readonly IEmployeeService _employeeService;

    public HomeController(IUnitOfWorkService unitOfWorkService) : base(unitOfWorkService)
    {
        _employeeService = unitOfWorkService.EmployeeService;
    }

    public ActionResult Index()
    {
        var emp = _employeeService.GetEmployee(employeeId);
        ...
    }

    ...
}  




I don't see a reason here to have private readonly IEmployeeService _employeeService; in the HomeController. It would be better to make the _employeeService variable of the BaseController protected so it can be used by the objects which inherits the BaseController.  
Why is the protected IUnitOfWorkService UnitOfWorkService; not readonly ?  




Style  


Using abbreviations or naming variables is bad practice. Does it hurt to name the variable IEmployeeRepository _employeeRepo like IEmployeeRepository _employeeRepository ?  
It does not hurt to use braces {} for single if statements but will make the code less error prone. I would like to encourage you to always use them.