I have been having permalink problems and I have narrowed it down to what I believe is the fix. I have multiple things using an .htaccess file which is the same one wordpress is trying to use. I figure if I am able to create an .htaccess file specifically for wordpress in a separate area from the other programs all problems will be fixed. However, I am not sure how to tell wordpress where the new location of the .htaccess file it should use is. I'm pretty knowledgeable in programming but am not sure where to put in the data to tell it it's new location for .htaccess.
Thanks