While the scenario you describe would work, the "best practice" approach is to not run any roles on the Hyper-V host other than Hyper-V; all services should run on virtual machines running on the Hyper-V host.
The hardware you describe should be more than capable of running three Hyper-V hosts; especially since a dedicated DC for 13 users would require minimal disk and memory resources.
The best option would be to obtain a single Windows Server 2008 R2 Enterprise license; this would entitle you to install the Hyper-V role on the hardware as well as up to four additional virtual instances of Windows Server 2008 R2 running on your Hyper-V host with no additional licensing cost.
If, however, you plan to use existing licenses for your application and file servers, another option would be to install Hyper-V Server 2008 R2 on the hardware to host your virtual servers. Hyper-V Server is free to download and use; however, no licensing is included, so any virtual machines you create must be individually licensed. Hyper-V Server is based upon Server Core, so the footprint and exposed surface area are very small. The UI provided with Hyper-V Server will assist in configuration of the machine for remote management; in this scenario, you will create and manage virtual machines on Hyper-V Server using the Hyper-V Manager MMC from your workstation. (Microsoft provides good information on this topic in the Microsoft Hyper-V Server 2008 R2 Getting Started Guide)