Just so you have a better idea of what I was referring to, here's just a small example..
RewriteEngine On
## Some site name here
RewriteRule ^some rule$ here
## #####
## Some other site name here
RewriteRule ^another rule$ here
RewriteRule somethingelse$ here
## #####
Then it's just a matter of in PHP adhering to the proper format, and when deleting an area, you just delete the areas between "## sitename" and "## #####". Easy to navigate, easy to work with.