Currently, there is no way to select what field to use to identify waypoinT id's. The tool simply uses shapefile name and the ObjectID (not helpful).
Trimble, mapping (maybe PFO group) invented per requests the Shape2Wpt, which this tool in positions is not close to its capability.
I've attached it You run the tool, and you will see the ability to crosswalk a field. Most notably, it has a slot for Select a "shapfile field for waypoint names".
Please, provide this in the next version. Waypoints in TerraSync are a key factor in setting that software apart. allow the user to select one field to assign waypoint name too.