Hi Matt,
Rather than use the tracklog, you should probably create a shapefile in ArcMap, run that through GPS Analyst to get it ready to work with GPScorrect in ArcPad.
Then when you are in ArcPad, turn on averaging for the gps collection. Then you can bring the data back into ArcMap using GPS Analyst.
Let me know how you go.
Cheers,
Gareth