Help with update from 1.5.3.1 to 1.5.4.1

Hello this is probably a dumb question.

Okay here is what happen. I made a copy of my site and put it on a different sub domain name. While i was working on the update on the sub domain. I got new orders with new customer from the main domain site witch is fine. The problem is I have now finished making all the changes needed to the sub domain witch i intended to use that data base for the upgrade. I am stuck. Cause I am not sure how to go about the upgrade.

Can I just copy all the files from the sub domain and use the install to do the upgrade? or

Can I just add the new customers to the new data base alonge with there orders?

Thanks for the help

Read this guide
http://www.opencart.com/index.php?route ... on&path=98