You set your initial timing exactly like you would any other distributor. Determine what total timing you want (usualy around 38 degrees), take the total mechanical timing of the distributor, subtract it from the desired total timing and set your initial there.
For example, if you want a total of 38 degrees and the distibutor has 28 degrees total, set the initial to 10 degrees BTDC.
On an MSD, the total timing is determined by the bushing size (bolted to the bottom of the breaker plate and the bushings are color coded). Red=28 degrees advance, Silver=25, Blue=21, and Black=18.
You can also change the springs on the weights to configure how fast your timing comes in. MSD are really cool in how configurable they are and how simple it is to configure them.