[SOLVED] Changing URLs using Atahualpa and Wordpress - only the index works

I apologize if this is an inappropriate question; I think it is more related to wordpress then the theme but just in case anyone has advice...

I have a non-wordpress website. I just developed a new website using wordpress as a cms and atahualpa as my theme. I want to move the new website to the domain.

I have the current website under: http://domain.com/en

My new wordpress version is under: http://domain.com/new/en

I've done the switch, keeping all the old pages in the directory /en, but adding the wordpress files and swapping out the indexes. I've now switched it back to the original index, because after doing the switch, only the new index shows - nothing else. The links appear to have all changed (I made the switch after changing the general settings to the new site directory in the dashboard)... but no luck getting any pages to work except the index.

Any advice?