Jared,
The MM6 is capable of a real-time accuracy of 2-5 meters when using SBAS (WAAS) for corrections. Post-Processing will improve that to sub-meter. Ashtech (formerly Magellan) developed an extension called GPSDifferential for ArcPad for post-processing, which collects raw data associated with the shapefiles.
Do you currently have GPSDifferential for ArcPad? If so, you will be able to collect your data in ArcPad with GPSDiffential for ArcPad recording raw data. Once the data is collected you will use MobileMapper Office to process the data.
You do not need to utilize an external antenna with the MM6 unit.
Feel free to email me if you should have any additional questions.