It has been a while since I analyzed this, but the technology should still work. ArcGIS Mobile uses your feature class design. If you add a binary field to your feature class, you can use that field to store an .ssf file for each collected feature. This is somewhat inefficient because you want to process just one .ssf file when you get back to the office. However, with this pattern you will have both the original feature and the information necessary for post-processing and they will be automatically synchronized with your server. Once the data are on the server, you will need to develop a tool to automate the processing. I believe that Paul York at Alsea Geospatial has successfully implemented this model.
