When you create a new project in Tuner Studio for your motor, it will over write what ever tunes are on the MS.
However, if the hardware is configured for his VR6 Golf, you will probably have to remove those configurations and set them up for the SW20, which could involve some soldering and research :)
Just to give you some information on identifying what version of MS your mate has. There are 3 processor versions (excluding MicroSquirt), MS1, MS2 & MS3 which plug into 3 PCB designs (excluding DIYPNP, MSPNP & MS3PRO).
The MS1 is just a simple processor chip that plugs into the PCB, it looks like this:

The MS2 is more of a daughter board design and has a more powerful processor and some extra hardware on the board. It looks like this:

The MS3, like the MS2 has a bigger processor, more hardware and features on it (SD card & USB) and looks like this:
The 3 version of PCB's are 2.2, 3.0 & 3.57.
The v2.2 board was the original design for the MS1, it is a through hole designed board which you can assemble yourself. The v2.2 lacks some more advanced circuits on the board (flyback circuits for low-z injectors) but can still be used for simple installs without any issues. They look like this:
The V3.0 board had a number of upgrades to the design, yet still maintained the through hole designs. They look like this:

.
The V3.57 board is essentially the same as the V3.0, but it uses surface mounted components (SMD, not through hole), which is easier to production run but not as easy for the average person to tinker with (if you get into modifying circuits). they look like this:
If the unit your friend has is indeed a MS3 v3.57, you might want to pick up an MS3X board (
http://www.diyautotune.co...nsion-card-p-434.html) to go with it, this will expand it's capabilities so you can run sequential fuel and spark on up to 8 cylinders plus have a range of other input/outputs at your disposal.
In the future, I'm looking at buying an MS3Pro for my 1MZFE V6 build :)