Ok I’ve managed to get my site into the root directory on my server so now have 2 copies as the original one is still in store.
If I work on the store copy can I back it up and use the backup to update the root version ??
So long as the sql points to the same place and the config.php file stays the same, I think so.
wetdec - yes - your store copy becomes your testing area etc - ensure no live links from other websites or search engines can access the store folder - should ensure you have a no follow in the meta area of the site.
since the mysql tables will be the same on both root and store - you can for backup purposes move back and forth - but once the store is live, the data will change on the root database and therefore you will need to be careful moving the database tables from one to the other - as for the tpl and php files - should be 100% no trouble to move a modified file from the store folder into the corresponding root folder
good luck - and always make a backup of your root level file before you do make a change 