First i would install backupmenu http://talk.maemo.org/showthread.php?t=63975 , then i would backup the settings and application to some external media.
Have your Linux-PC or a Linux-Live-CD ready to repartition the N900.
Next do a reboot of the N900 to backupmenu, switch read/write USB mode on and repartition the device to the needed layout after right after flashing. Then i would apply the backup.
Here is the wiki about repartitioning: http://wiki.maemo.org/Repartitioning..._compatible.29