always use internal drives for your boot disk and storage disks you wanted associated with the computer.
externals are meant for either a backup disk, network accessable storage disk, or portable disk to take with you on the go. they are not suggested to replace the role of an internal drive.
if you go with a western digital caviar black, go with the 1tb model instead of the 1.5tb as the latter one has issues (3 dead drives on me so far!) i've heard decent things about the spinpoints.