Currently I have a rewrite rule to redirect you to the subfolder that has the website in it
(www.dejongetestsite.site refers to www.dejongetestsite.site/TKLive2/upload)
but as soon as I click another page it adds the subfolders back in. I can manually enter http://www.dejongetestsite.site/store and it works like it should. Is there another rule that I can write that will remove the /TKLive2/upload from all urls
Please take the time to read the PHP Manual on the substr function. The manual is your friend.
Aside from that, I ran this in my browser
$string = "www.dejongetestsite.site/TKLive2/upload";
$string = substr($string, 0, -15);
echo $string;
And it outputs
www.dejongetestsite.site
As for .htaccess, I think (don't quote me) it may be this?
RewriteEngine On
RewriteRule ^/TKLive2/(.*)$ http://www.dejongetestsite.site/$1 [L,R=301]