Permalinks not working

I am using the WP loop on my home page, just to retrieve the posts. The problem is none of the permalinks work, I just get page not found.

I presume this is because I have WP_USE_THEMES set to false because I have my own design I am trying to integrate it into. However, surely this needs to be linked to the single.php or something, which it probably isn’t doing. How do I get my WP loop to still connect to the rest of the template as usual, even though I have WP_USE_THEMES off?

P.S. It would help if someone could explain where and how the single.php page is called. I can’t find anything in the code of the process when single.php is called with whatever post id needs to be passed.

– all my template files exist and none have been edited.
– no syntax errors anywhere.
– no permissions problems.