from the Terminal app, or ADB commands.
Its best to use ext3 on your SD Card.
DT Commands:
*a2db shell ("su" in Terminal Emulator)
*a2sd check
*a2sd reinstall
reboot
*a2sd zipalign
*a2sd cachesd
reboot
On my N1 work fine after these commands
Sorry for my english, I'm italian :D