Transferring a modified atahualpa theme from one site to another

I'm sure I'm missing something obvious here! I just designed a new site in Atahualpa - but it was installed on a test sub-domain. Now I want to transfer the custom design to a new site.

This is what I tried:
Using ftp software to download the entire Atahualpa folder to my computer (from the customised sub site).
Installing WP and Atahualpa on the new site.
Using ftp software to upload the entire Atahualpa folder from my computer to the new site.

It failed! The new site still looks like a fresh install.

I guess what's stumped me is - where is Atahualpa saving all those changes I made?