From: DeskNow Knowledge Base
http://www.desknow.com/kb/

How do I migrate from the old McKoi database to an external database?
http://www.desknow.com/kb/idx/9/132/article/
This article applies to DeskNow 3.1 and later

Please note: depending on the amount of data existing on your system, the migration could take some time (even 2 hours on large installations). It is recommended to perform this operation at night time or during the weekend.

If you're using DeskNow on Windows, installed with the default installer (DeskNow.exe)

  1. Make sure to run DeskNow 3.1 or later as usual - if you upgrade from a previous release, make sure it runs at least once using McKoi
  2. stop DeskNow
  3. edit the Database.cfg file (from the 'Manual configuration' section in the DeskNow program group) and add the following line:
    Migrate TRUE

    then save the file and close Notepad
  4. start DeskNow in console (see the 'Advanced' section in the DeskNow program group)
  5. open the login page in your browser
  6. watch the migration process take place in the console window
  7. once the login page appears in the browser, stop DeskNow
  8. start DeskNow as usual

If you're using DeskNow on Linux, or you want to use your own database even on Windows

  1. Make sure to run DeskNow 3.1 or later as usual - if you upgrade from a previous release, make sure it runs at least once using McKoi
  2. stop DeskNow
  3. edit the Database.cfg file and add the following line:
    MigrateExternal TRUE

    then save the file
  4. start DeskNow in console (ex. /var/desknow/bin/catalina.sh run)
  5. open the login page in your browser, and configure the external database to be used.
  6. watch the migration process take place in the console window
  7. once the login page appear in the browser, stop DeskNow (CTRL-C)  
  8. start DeskNow as usual