using mod_rewrite for menu links

I want to use mod_rewrite to hide the location of my wordpress files, so they are not exposed in the URI. When I set custom links for menu items in the Wardpress dashboard and then add my rewrite rules to the .htaccess file below what Wrodpress has put in the file, the rewrite fails. I suspect i has something to do with the way that WordPress itself uses mod_rewrite. Can anyone help me figure out how to do what I want to do. I’ve spent a bunch of hours with it and am stumped.

I find it hard to follow the WordPress code from script to script. I wonder if there is a map or some good documentation if the wordpress coding flow to help me figure out what is done where. It is especially confusing what gets done in a theme folder and what gets done by the master wordpress scripts. It is a bit of spaghetti code. I wonder if wordpress is ever going to do what Drupal did and convert everything to clean OOP code.

Thanks,

–Kenoli