Support

Once i am ready to go live can i just make a backup and load this into the root?

Almost. Take a backup, remove the old files and directories from the site's root, then restore the backup in the site's root. If you skip the part in bold letters you will end up with a broken site.

Also just to confirm with restoring a backup does the joomla version need to be the same? 

This is quite ambiguous. If you intend to restore a backup on top of an existing site then the Joomla! version must match. Otherwise there's a big chance that your site will be broken to changes in core Joomla! files layout.

I am going to assume it just overwrites itself when you try and restore from the backup?

Not exactly. We NEVER remove any files or folders. We only overwrite files which exist both on the disk and the backup. If you are restoring on top of a different Joomla! version the files present on disk but not present in the archive are not removed. This is why you shouldn't, for example, restore a Joomla! 2.5 site's backup on top of a Joomla! 1.5 site (or vice versa).

Is there going to be any issues with admin tools permissions etc?

I don't understand what you are asking. If you mean file permissions, you can of course use Admin Tools to modify them. File ownership cannot be modified, of course.

htaaccess? or even the fact that it is in a new directory or with the process fix itself in the process?

This is something you have to take care yourself. After the restoration is finished, remove the .htaccess using FTP. Then log in to your site's back-end and go to Components, Admin Tools, .htaccess Maker. Scroll down to the bottom of the page. Change the directory to a single forward slash: / Then click on Save and Create .htaccess. Admin Tools doesn't know that your site's directory has changed. This is the way you let it know of this change.