Do htaccess / chmod rules exclude each other?

Hi, I had a website hacked the other day, and the hosting’s support guy told me that the security of my website was weak; So he recommended change the default names fot the wordpress system; I renamed the wp-content folder name, but can’t change (efficiently) the wp-admin folder name; so I secured it by using htaccess rules. But I secured it so much, that the images used by the site were blocked. So, I changed the chmod for the upload folder. Then came the doubt: If I secure a folder using chmod, does this override the htaccess settings? Which one of these two settings is more reliable? I think they might work on different levels, but I don’t really know which is more secure.