Okay im going to go back and redo all of that and start fresh.
I redid the sub domain and its working now.
The site shows up as harpermoto.com/manuals/index.php
My next question I have though is since I would like to use the complete same layout as my main site, such as the background and what not, can I copy the whole entire my_changes folder from my main site over the the sub domain directory?