.htacces expert, mod_rewrite in subfolder

I install a new cms (phpmydirectory) in a subfolder. In the root there is a wordpress with friendly url's. When I activate the friendly url's in phpmydirectory, I get an 404 error in the categories and locations, but no in the listings. The 404 error appear in the blog template and URL. I need to fix the -htaccess so the subfolder read the .htaccess in the subfolder ando no the one in root.