Unless you fill up the harddrive a lot fragmentation is usually no problem for ext3. And the pure unslung system with mt-daapd needs not that much space in view of the 160 GB harddrives of today. So leave 20% empty and fill the rest with mp3s, if the drive is already correctly formatted in ext3.
Filling the HD via USB is anyway the best as it takes ages to fill 100GB via network.