The advantage of extended partitions is that if you want to you can carve it up into smaller partitions again so that it looks like your single partition is actually several. The partition with your OS must be a primary, but if you're chucking this drive in a caddy I'm guessing that's not the case. Far as I remember only one Primary will be visible at a time, so use an extended.
EDIT: Practically rewrote the post with better (?) info.