Upload Files to the Production Server
Go to the Perpetua Console and click on the staging site from the list of sites. In the list on the right, click on Dynamic Email Pages. These are all the pages of the sites and their corresponding page IDs. From this screen make a note of the page ID number next to the Welcome page and the page ID of the next page in the list. Rename your home page layout file with the Welcome page ID (i.e. change _layout_1.cfm to _layout_#newNumber#.cfm). Do the same with the Email page and the second listed page ID (i.e. change _layout_email.cfm to _layout_#newNumber#.cfm).
In Coda, right click the HTML folder on your local side and go to Publish > Mark for Publishing. Then, within the Publish pane of Coda, click Publish to upload the folders and files without overwriting the files generated by Perpetua.
Assign Dynamic Email Page
After you have adjusted the created and renamed the layout file for the dynamic email, go back to the Perpetua Console and Click on Dynamic Email Pages again. For the page ID that you have assigned and created the layout for the Email, click the check box next to that page. Then click save. Go to your staging site and login. Now go to the actual page by typing in http://#your staging site domain#/index.cfm/pageid/#your email's page id number# and under Page Properties > Basic, reassign the name of the page to say Email.