1. First Backup all your site content and database.
2. In PHPMyadmin of your hosting select the database table ebayclone_categories and drop it if you want the default categories from seo version else, edit your category names excluding special characters and spaces, eg: Arts & Antiques must be edited as Arts-Antiques for seo urls to work correctly.
3. Replace all php-files and only selectively replace the design files(theme/default). You can also duplicate a theme eg: default1 and copy all theme files from seo version to this folder and select this theme from admin or you can copy only the style.css and images files from your old theme to this new theme.
The theme files to add/replace are: browsecats.tpl, browse.tpl, item.tpl, home.tpl, global_header
If you have made changes to your php files, You can try replacing only these selective files:
root folder: browse.php, header.php index.php, item.php, seoheader.php, seo_cat_header.php, seo_item_header.php, .htaccess file.
includes folder: browseitems.inc
themes/default: already mentioned above.