since there have been no other posts I will tell you what I have got to work. It's probably the long way to go about it, but here it is anyway.
I created a user for the website and made that user part of the apache group. This user only has ftp access, and it's home directory is the same as the the root of the website.
Say I have my html files in /var/www/html and I have 2 subdirectories in the html directory called sub1 and sub 2, you'd do the following. I'll call the user "website".
Code:
cd /var/www
chown website html
cd html
chown website *
cd sub1
chown website *
cd ../sub2
chown website *
Hope this helps, and maybe someone can tell us a better way to do this.