You can change the diskconfiguration to the way that you want it. However I think that you have an exaggerated idea of what parted will do. You will use parted to set up the partitions on the new disk. Then you use other commands to format the partitions, copy files to the new disk, change /etc/fstab, and change /etc/lilo.conf.
After you get your new disk set up and working then you will save the data on the old disk somewhere on the new disk. Then use parted to reconfigure the partitions on the old drive. Then format the partitions on the old drive, copy files to the old disk, etc.
Be prepared. Create a LifeBoat CD.