If you see the error message:
fsck does not want to work because /dev/md0 is in use
and the boot process drops to a shell, your drives will be mounted as read-only. In order to mount them so you can write to them you can remount the filesystem in read/write mode with:
sudo mount -o remount,rw /
You could try also unmounting the drives and running fsck manually on them:
umount / fsck /dev/md0
Then, if everything is OK, reboot.