I would put the hard drive you currently have in the Macbook in the external enclosure. Then put the new drive in the Macbook. Install OS X on the new internal drive. Then, when you start up for the first time and it asks you if you want to migrate your data from a previous mac, say yes. Connect the external drive to the Macbook through USB or firewire, and it'll put everything where it's suppose to go.
I hope that makes sense.