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1. Once you've finished collecting data, save and close your Map Project in ArcPad on the GPS unit. 
2. Exit ArcPad, but leave the GPS unit on.
3. Doc the GPS unit and connect it to the computer.
4. Open the ArcMap Project you collected data for in ArcMap.
5. Go to Start → My Computer → Other → Mobile Device → DataForArcPad.  You will see files in the folder that have the names of  layers from your Map Project. They follow these formats:
   
   ProjectName_gdb.axf
   
   
6. Copy this file to the ActiveSync folder you used for your Output Options during the Check Out process.  The folder should look something like this: "I:\YourDrewUsername\My Documents\Geo4939435713 My Documents\MapProjectName."  You will be asked if you want to replace the existing files in the folder with the files you are copying from the GPS unit.  Click "Yes."
7. In your ArcMap project, open and editing session using the Editor tool bar.
8. Click on the Get Data From ArcPad button in the ArcPad Data Manager tool bar.  The Get Data from ArcPad dialog box will appear.
9. If your data files do not appear in the dialog box, click on the button with the green plus sign in the top, right hand corner of the dialog box.
10. Navigate to the ActiveSync folder with the newly copied data.  Select the .axf file you copied from the GPS unit.  If you edited data, you will see that it has been Modified in the Feature Class/Table area.  If you added new data, you will see that there are items under the Added column in the Feature Class/Table area.
11. Check the box next to the .axf file.
12. Click Check In.  You will be asked if you want to check in the selected data. 
13. Click Yes.  A Get Data from ArcPad dialog box will appear with the Check In results. 
14. Click OK.
15. Close the Data from ArcPad dialog box.
16. Save your Edits in the Editor tool bar. 
17. Stop the editing session.
18. Save the Map Project.
19. Close the Map Project.
20. Navigate to I: → YourDrewUsername → My Documents → Geo4939435713 My Documents.  Delete the folder for the data you just checked in.  ArcMap will not allow you to overwrite a folder during hte Check Out process, so you must delete folders from your ActiveSync folder in order to continue to use the same project folder name.

Adapted from the ESRI Knowledge Base article, "What is the difference between the ArcPad toolbar and the ArcPad Data Manager toolbar?" accessed July 1, 2011 from http://support.esri.com/en/knowledgebase/techarticles/detail/36035.