Moving a site

I currently have a Joomla site installed on my VPS. We will call it

I have developed a WordPress site that is going to replace it in the coming days. It is located at

I am worried about the absolute links that wordpress requires for images, links etc. If I FTP into my site and move all the contents of the wp/ folder into the root folder, I believe everything should be ok right? or would it be better to point the domain name to The problem I see with this would be that when I then FTP in, would I bypass the old site’s documents all together? or would I still navigate to

Little confused on the best course here. Please be detailed in any replies.