Okay, I found somewhat of a solution to my own problem, so I thought I’d post it just in case someone had a similar problem.
In the base settings, I defined the $siteurl variable to be a page name like “index.php” and left the $blogfilename variable blank. This creates archive links that are relative and just go to index.php/?p=1 etc. Not the best code, but it works for me since all that pages that call content reside in their own subdirectories and are called “index.php”