I also have a project with layers linking to a common table, but in this case there are mutiple layers connected to multiple common tables. Our old ArcPad 8 application used custom scripts to write data to the tables, and there was a lot of post-processing after check-in on the desktop.
For ArcPad 10, we wanted to take advantage of the related table functionality, so we redesigned our geodatabase schema. There are now separate copies of each table linked to each layer. During check-in, there is a simple tool that appends the data from the appropriate tables back into the master table. This was the best solution in term of record management. But the AXF file is rather large, and is running slower than the old application.
With just one table, I think a similar approach would work out well.