Installing add-ons rarely disturb existing data in your database. Some, needing to store data related to the add-on simply create additional tables in the database and do not affect existing data. When data must be added or changed in existing tables, most add-on's provide the sql script to accomplish this.
Here is a simple method which should work:
Always backup both the website files and the mySql database files of both the old and new version of your website before you start.
In this case I am suggesting you simply replace the old Zencart files with the new ones from your subdomain so that your website keeps the same url.
1. Copy your backup of your subdomain into your existing webroot (in otherwords, copy them over your current website files.) Make sure the includes/configure.php and admin/includes/configure.php permissions are set to "read only" (-r-r-r- or 444) on the current site. This will prevent replacing these files with those from the subdomain (you must retain the configuration settings of the current website.) As a precaution, you might also want to rename these files in the subdomain backup before copying the fileset to the main domain).
So to review: you are going to copy your fileset from the subdomain into the main domain but retain the two configure.php files of the existing website.
2. You will continue to use the existing database associated with the current website on the main domain. Check the installation files of the add-ons that were added to the subdomain for any sql files and run them on the main domain. Do not run sql files for add-ons that pre-existed on the main domain. This will update your existing database for the add-on features.
3. If some of the add-ons required you to make settings in admin after running the sql files, then you should check and re-enter those settings.



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