Hey Riza,
I think you are missing something.
From NAV 5 TO NAV 6 / 6SP1 / 6 R2 there is no data migration required, only technical merging need to be done.
The Data Migration Upgrade Tool is available from NAV 3.7 or 4.3 to NAV 2009.
If you are using NAV 5.0 you need to follow these steps -
1. Do Technical Merging. (Object Merging)
2. Open the Client Database in Version 2009 / 2009 SP1 / 2009 R2.
3. Convert the Database.
4. Delete all objects except tables.
5. Import & replace New Merged Objects Completed in Step 1.
Steps are listed in the NAV 2009 / NAV 2009 SP1 / NAV 2009 R2 DVD at below location -
UpgradeToolKit\Documents\Upgrade Quickguides Upgrade Quick Guide 500_2009.doc
Let me know if any doubts.